A manual and introductory tutorial }
-\vspace{2.5in}
+\vspace{2.4in}
{\large
-David Martin, James Procter, Andrew Waterhouse and Geoff Barton
+David Martin, James Procter, Andrew Waterhouse, Saif Shehata and Geoff Barton
}
-\vspace{1.5in}
+\vspace{1.2in}
College of Life Sciences, University of Dundee
\vspace{2in}
-Manual version 1.3
+Manual version 1.3.02
-30th November 2011
+25th June 2012
\end{center}
-\clearemptydoublepage
+\newpage
+
+% \clearemptydoublepage
% ($Revision$) 11th October 2010.}
% TODO revise for 2.6
This paper supersedes the original Jalview publication:\newline {\sl ``The Jalview Java alignment
editor"} \newline Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey J. Barton (2004) \newline {\sl Bioinformatics} {\bf 20} 426-427.
- \r\subsection{About this tutorial }
+
+\subsection{About this tutorial }
This tutorial is written in a manual format with short exercises where
appropriate, typically at the end of each section. This chapter concerns the
\subsubsection{Typographic Conventions}
Keystrokes using the special non-symbol keys are represented in the tutorial by enclosing the pressed keys with square brackets ({\em e.g.} [RETURN] or [CTRL]). Keystroke combinations are combined with a `-' symbol ({\em e.g.} [CTRL]-C means press [CTRL] and the `C' key). Menu options are given as a path from the menu that contains them - for example {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} means to select the `From URL' option from the `Input Alignment' submenu of a window's `File' dropdown menu.
-\r\section{Obtaining and starting The Jalview Desktop Application}
+
+\section{Obtaining and starting The Jalview Desktop Application}
\label{startingjv}
\begin{figure}[htbp]
\begin{center}
production of publication quality graphics.
The Jalview Desktop can be run in two ways; as an application launched from the
-web via Java Web Start, or as an application loaded onto your hard drive. Both
-versions are obtained from the Download page at the the Jalview web site
+web {\sl via} Java Web Start, or as an application loaded onto your hard drive. Both
+versions are obtained from the Download page at the Jalview web site
(http://www.jalview.org/).
Jalview can be started directly with webstart by navigating to the Download page
-(via the menu on the left hand side), and clicking the `Start with Java Webstart'
+({\sl via} the menu on the left hand side), and clicking the `Start with Java Webstart'
button. (Figure \ref{download}). This will always launch the latest stable
release of Jalview.\par
\label{splash}
\end{center}
\end{figure}
-\rWhen Jalview starts it will automatically load an example alignment from the
+
+When Jalview starts it will automatically load an example alignment from the
Jalview site. This behaviour can be changed in the Jalview Desktop preferences
dialog opened from the Desktop's {\sl Tools $\Rightarrow$ Preferences..} menu.
This alignment will look like the one in Figure \ref{startpage} (this is taken
From time to time, important announcements are made available to users of the
Jalview Destop {\sl via} the Jalview News reader. This window will open
-automatically when new news is available, and can also be accessed via the
+automatically when new news is available, and can also be accessed {\sl via} the
Desktop's `{\sl Tools $\Rightarrow$ Show Jalview News}' menu entry.
\begin{figure}[htbp]
\subsubsection{Email lists}
The Jalview Discussion list {\tt jalview-discuss@jalview.org} provides a forum for Jalview users and developers to raise problems and exchange ideas - any problems, bugs, and requests for help should be raised here. The {\tt jalview-announce@jalview.org} list can also be subscribed to if you wish to be kept informed of new releases and developments. Archives and mailing list subscription details can be found on the Jalview web site.
-\r\section{Navigation}
+
+\section{Navigation}
\label{jvnavigation}
The major features of the Jalview Desktop are illustrated in Figure \ref{anatomy}. The alignment window is the primary window for editing and visualization, and can contain several independent views of the alignment being worked with. The other windows (Trees, Structures, PCA plots, etc) are linked to a specific alignment view. Each area of the alignment window has a separate context menu accessed by clicking the right mouse button.
\end{figure}
\subsection{Navigation in Normal mode}
-\rJalview always starts up in Normal mode, where the mouse is used to interact with the displayed alignment view. You can move about the alignment by clicking and dragging the ruler scroll bar to move horizontally, or by clicking and dragging the alignment scroll bar to the right of the alignment to move vertically. If all the rows or columns in the alignment are displayed, the scroll bars will not be visible.\r\r Each alignment view shown in the alignment window presents a window onto the visible regions of the alignment. This means that with anything more than a few residues or sequences, alignments can become difficult to visualize on the screen because only a small area can be shown at a time. It can help, especially when examining a large alignment, to have an overview of the whole alignment. Select {\sl View $\Rightarrow$ Overview Window} from the window menu (Figure \ref{overview}).\r%(Figure4)
+
+Jalview always starts up in Normal mode, where the mouse is used to interact with the displayed alignment view. You can move about the alignment by clicking and dragging the ruler scroll bar to move horizontally, or by clicking and dragging the alignment scroll bar to the right of the alignment to move vertically. If all the rows or columns in the alignment are displayed, the scroll bars will not be visible.
+
+ Each alignment view shown in the alignment window presents a window onto the visible regions of the alignment. This means that with anything more than a few residues or sequences, alignments can become difficult to visualize on the screen because only a small area can be shown at a time. It can help, especially when examining a large alignment, to have an overview of the whole alignment. Select {\sl View $\Rightarrow$ Overview Window} from the window menu (Figure \ref{overview}).
+%(Figure4)
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/overview.pdf}
\label{overview}
\end{center}
\end{figure}
-\rThe red box in the overview window shows the current view in the alignment window. A percent identity histogram is plotted below the alignment overview. Shaded parts indicate rows and columns of the alignment that are hidden (in this case, a single row at the bottom of the alignment - see Section \ref{hidingregions}). You can navigate around the alignment by dragging the red box. %Try this now and see how the view in the alignment window changes.\r\r\parbox[c]{3in}{Alignment and analysis windows are closed by clicking on the usual `close' icon (indicated by arrows on Mac OS X). If you want to close all the alignments and analysis windows at once, then use the {\sl Window $\Rightarrow$ Close All} option from the Jalview desktop (\em{warning: make sure you have saved your work because this cannot be undone !}). }
+
+The red box in the overview window shows the current view in the alignment window. A percent identity histogram is plotted below the alignment overview. Shaded parts indicate rows and columns of the alignment that are hidden (in this case, a single row at the bottom of the alignment - see Section \ref{hidingregions}). You can navigate around the alignment by dragging the red box. %Try this now and see how the view in the alignment window changes.
+
+\parbox[c]{3in}{Alignment and analysis windows are closed by clicking on the usual `close' icon (indicated by arrows on Mac OS X). If you want to close all the alignments and analysis windows at once, then use the {\sl Window $\Rightarrow$ Close All} option from the Jalview desktop (\em{warning: make sure you have saved your work because this cannot be undone !}). }
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
%TODO insert a figure for the Find dialog box
-\r\section{Loading your own sequences}\r\label{loadingseqs}\rJalview provides many ways to load your own sequences. %For this section of the tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.\r\r\subsection{Drag and Drop}\r In most operating systems you can just drag a file icon from a file browser\r window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended\rto that alignment. Drag and drop also works when loading data from a URL -\rsimply drag the link or url from the address panel of your browser on to an\ralignment or the Jalview desktop background and Jalview will load data from the\rURL directly.\r% (Figure \ref{drag})
-% %[fig 5]\r% \begin{figure}[htbp]\r% \begin{center}\r% \includegraphics[width=2in]{images/drag2.pdf}\r% \includegraphics[width=2in]{images/drag3.pdf}\r% \caption{{\bf An alignment can be opened by dragging the file onto the Jalview window. }}\r% \label{drag}\r% \end{center}\r% \end{figure}\r% \r% %\includegraphics[width=2in]{images/drag1.pdf}
-\r\subsection{From a File}\r Jalview can read sequence alignments from a sequence alignment file. This is a text file, not a word processor document. For entering sequences from a wordprocessor document see Cut and Paste (Section \ref{cutpaste}) below. Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu (Figure \ref{loadfile}). You will then get a file selection window where you can choose the file to open. Remember to select the appropriate file type. Jalview can automatically identify some sequence file formats.\r\r%[fig 6]\r\begin{figure}[htbp]
+\section{Loading your own sequences}
+\label{loadingseqs}
+Jalview provides many ways to load your own sequences. %For this section of the tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
+
+\subsection{Drag and Drop}
+ In most operating systems you can just drag a file icon from a file browser
+ window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended
+to that alignment. Drag and drop also works when loading data from a URL -
+simply drag the link or url from the address panel of your browser on to an
+alignment or the Jalview desktop background and Jalview will load data from the
+URL directly.
+% (Figure \ref{drag})
+% %[fig 5]
+% \begin{figure}[htbp]
+% \begin{center}
+% \includegraphics[width=2in]{images/drag2.pdf}
+% \includegraphics[width=2in]{images/drag3.pdf}
+% \caption{{\bf An alignment can be opened by dragging the file onto the Jalview window. }}
+% \label{drag}
+% \end{center}
+% \end{figure}
+%
+% %\includegraphics[width=2in]{images/drag1.pdf}
+
+
+\subsection{From a File}
+ Jalview can read sequence alignments from a sequence alignment file. This is a text file, not a word processor document. For entering sequences from a wordprocessor document see Cut and Paste (Section \ref{cutpaste}) below. Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu (Figure \ref{loadfile}). You will then get a file selection window where you can choose the file to open. Remember to select the appropriate file type. Jalview can automatically identify some sequence file formats.
+
+%[fig 6]
+\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2in]{images/loadfilebox.pdf}
%\includegraphics[width=2in]{images/loadfilebox2.pdf}
\label{loadfile}
\end{center}
\end{figure}
-\r\subsection{From a URL}\r Jalview can read sequence alignments directly from a URL. Please note that the files must be in a sequence alignment format - a pretty HTML alignment or graphics file cannot be read by Jalview. \rSelect {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and a window will appear asking you to enter the URL (Figure\ref{loadurl}). Jalview will attempt to automatically discover the file format.\r\r%[fig 7]
+
+\subsection{From a URL}
+ Jalview can read sequence alignments directly from a URL. Please note that the files must be in a sequence alignment format - an HTML alignment or graphics file cannot be read by Jalview.
+Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and a window will appear asking you to enter the URL (Figure \ref{loadurl}). Jalview will attempt to automatically discover the file format.
+
+%[fig 7]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2in]{images/menuloadurl.pdf}
\label{loadurl}
\end{center}
\end{figure}
-\r\subsection{Cut and Paste}
-\label{cutpaste}\rDocuments such as those produced by Microsoft Word cannot be readily understood\rby Jalview. The way to read sequences from these documents is to select the\rdata from the document and copy it to the clipboard. There are two ways to\rdo this. One is to right-click on the desktop background, and select the\r`Paste to new alignment' option in the menu that appears. The other is to select\r{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the\rmain menu, and paste the sequences into the textbox window that will appear\r(Figure \ref{loadtext}). In both cases, presuming that they are in the right\rformat, Jalview will happily read them into a new alignment window.\r%[fig 8]
+
+\subsection{Cut and Paste}
+\label{cutpaste}
+Documents such as those produced by Microsoft Word cannot be readily understood
+by Jalview. The way to read sequences from these documents is to select the
+data from the document and copy it to the clipboard. There are two ways to
+do this. One is to right-click on the desktop background, and select the
+`Paste to new alignment' option in the menu that appears. The other is to select
+{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
+main menu, and paste the sequences into the textbox window that will appear
+(Figure \ref{loadtext}). In both cases, presuming that they are in the right
+format, Jalview will happily read them into a new alignment window.
+%[fig 8]
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\r\subsection{From a public database}
-\label{fetchseq}\rJalview can retrieve sequences and sequence alignments from the public
-databases housed at the European Bioinformatics Institute, such as Uniprot,\rPfam and the PDB, as well as any DAS sequence server registered at the\rconfigured DAS registry. This facility avoids having to manually locate, save\rand load the sequences, and allows Jalview to gather additional metadata\rprovided by the source, such as annotation and database cross references.\rSelect {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and\ra window will appear (Figure \ref{loadseq}). Use the menu box to select the\rappropriate database, enter a sequence ID/accession number, or several\rseparated by a semicolon and Jalview will attempt to retrieve it/them from the
-chosen database source. Example queries are provided to test that a source is\roperational, and can also be used as a guide for the type of accession numbers\runderstood by the source.\r%[fig 9]\r\begin{figure}[htbp]
+
+\subsection{From a public database}
+\label{fetchseq}
+Jalview can retrieve sequences and sequence alignments from the public
+databases housed at the European Bioinformatics Institute, such as Uniprot,
+Pfam and the PDB, as well as any DAS sequence server registered at the
+configured DAS registry. This facility avoids having to manually locate, save
+and load the sequences, and allows Jalview to gather additional metadata
+provided by the source, such as annotation and database cross references.
+Select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and
+a window will appear (Figure \ref{loadseq}). Use the menu box to select the
+appropriate database, enter one or several database IDs or accession numbers separated
+ by a semicolon and press OK. Jalview will then attempt to retrieve them from the chosen database. Example queries are provided for some
+databases to test that a source is operational, and can also be used as a guide
+for the type of accession numbers understood by the source.
+%[fig 9]
+\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2.5in]{images/fetchseq.pdf}
\caption{{\bf Retrieving sequences from a public database}}
\exercise{Loading sequences}{
\label{load}
-\exstep{Start Jalview then close all windows by selecting {\sl Window $\Rightarrow$ Close All} from the main menu}
-\exstep{Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box. Click {\sl OK} and the alignment should load.
+\exstep{Start Jalview then close all windows by selecting {\sl Window $\Rightarrow$ Close All} from the main menu.}
+\exstep{Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box. Click OK%jbp shouldn't this be sl
+and the alignment should load.
}
\exstep{Close all windows using the {\sl Window $\Rightarrow$ Close All} main
-menu option. Point your web browser at the same \href{http://www.jalview.org/tutorial/alignment.fa}{URL} and save the file to
-your desktop. Open this file in Jalview by selecting {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu and browsing to the appropriate location. Click OK and load the alignment }
-\exstep{Drag the alignment.fa file from the desktop onto the Jalview window. The
-alignment should open. Try dragging onto an empty Jalview and onto an existing
+menu option. Point your web browser at the same \href{http://www.jalview.org/tutorial/alignment.fa}{URL} and save the file to your desktop. Open this file in Jalview by selecting {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu and selecting the file from your desktop. Click OK and load the alignment.}
+\exstep{Select {\sl Window $\Rightarrow$ Close All} and drag the alignment.fa file from the desktop onto the Jalview window. The alignment should open. Try dragging onto an empty Jalview and onto an existing
alignment and observe the results. You can also try dragging the
\href{http://www.jalview.org/tutorial/alignment.fa}{URL} directly onto Jalview.
}
-\exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the {\sl PFAM (seed)} database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. }
-\exstep{Open the \href{http://www.jalview.org/tutorial/alignment.fa}{URL} in a
-web browser. Select and copy the entire text to the clipboard (usually via the
+\exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the PFAM seed database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. }
+\exstep{Open the \href{http://www.jalview.org/tutorial/alignment.fa}{URL} above in a
+web browser. Select and copy the entire text to the clipboard (usually {\sl via} the
browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running
and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} .
Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
Paste} text box menu option. Click {\sl New Window} and the alignment will be
-loaded. } }
+loaded. } }
\subsection{Memory Limits}
\label{memorylimits}
Tools $\Rightarrow$ Show Memory Usage} function, which enables the display of the
currently available memory at the bottom left hand side of the Desktop window's
background. Should you need to increase the amount of memory available to
-Jalview, full instructions are given in both the built in documentation and on
-the JVM memory parameters page (http://www.jalview.org/jvmmemoryparams.html) on
+Jalview, full instructions are given in the built in documentation (opened by selecting {\sl Help $\Rightarrow$ Documentation})
+and on the JVM memory parameters page (http://www.jalview.org/jvmmemoryparams.html) on
the website.
-\r\section{Writing sequence alignments}
+
+\section{Writing sequence alignments}
\label{savingalignments} \subsection{Saving the alignment} Jalview allows the
current sequence alignments to be saved to file so they can be restored at a
later date, passed to colleagues or analysed in other programs. From the
alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box
will appear (Figure \ref{savealign}). You can navigate to an appropriate
directory in which to save the alignment. Jalview will remember the last filename
-and format used to save (or load) the alignment, enabling you to quickly update
-the file after editing by using the {\sl File $\Rightarrow$ Save} entry.
+and format used to save (or load) the alignment, enabling you to quickly save
+the file during or after editing by using the {\sl File $\Rightarrow$ Save} entry.
+
+Jalview offers several different formats in which an alignment can be saved. The jalview format (.jar) is the only one which will preserve the colours, groupings and similar information in the alignment. The other formats produce text files containing just the sequences with no visualization information, although some allow limited annotation and sequence features to be stored (e.g. AMSA). Unfortunately only Jalview can read Jalview files. The {\sl File $\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into other documents or web servers.
-Jalview offers several different formats in which an alignment can be saved. The jalview format is the only one which will preserve the colours, groupings and similar information in the alignment. The other formats produce text files containing just the sequences with no visualization information, although some allow limited annotation and sequence features to be stored (e.g. AMSA). Unfortunately only Jalview can read Jalview files. The {\sl File $\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into other documents or web servers.
-\r%[fig 10]
+%[fig 10]
\begin{figure}[htbp]
\begin{center}
\parbox[c]{1.0in}{
\end{center}
\end{figure}
-\subsection{Jalview Projects}\r\parbox[c]{4in}{If you wish to save the complete Jalview session rather than just one alignment (e.g. because you have calculated trees or multiple different alignments) then your work should be saved as a Jalview Project file\footnote{Tip: Ensure that you have allocated plenty of memory to Jalview when working with large alignments in Jalview projects. See Section \protect \ref{memorylimits} above for how to do this.}.
+\subsection{Jalview Projects}
+\parbox[c]{4in}{If you wish to save the complete Jalview session rather than just one alignment (e.g. because you have calculated trees or multiple different alignments) then your work should be saved as a Jalview Project file\footnote{Tip: Ensure that you have allocated plenty of memory to Jalview when working with large alignments in Jalview projects. See Section \protect \ref{memorylimits} above for how to do this.}.
From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save dialog box will appear. Loading a project will restore Jalview to exactly the view at which the file was saved, complete with all alignments, trees, annotation and displayed structures rendered appropriately.
}
\parbox[c]{2in}{
\exercise{Saving Alignments}{
\label{save}
\exstep{Start Jalview, close all windows and load the ferredoxin alignment from
-PFAM (PFAM Seed accession number PF03460 (see Exercise \ref{load}). }
+PFAM (PFAM seed accession number PF03460 (see Exercise \ref{load}). }
\exstep{
-Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a location into which to save the alignment and select a format. All formats except {\sl Jalview } can be viewed in a normal text editor (e.g. Notepad) or in a web browser. Enter a file name and click {\sl Save}. Check this file by browsing to it with your web browser or by closing all windows and opening it with Jalview.
+Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a location into which to save the alignment and select a format. All formats except {\sl Jalview } can be viewed in a normal text editor (e.g. Notepad) or in a web browser. Enter a file name and click {\sl Save}. Check this file by closing all windows and opening it with Jalview or by
+browsing to it with your web browser.
}
\exstep{ Repeat the previous step trying different file formats.}
\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}. You can select and copy this alignment to the clipboard using the textbox menu options {\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}. The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
\exstep{Ensure at least one alignment window is shown in Jalview. Open the
overview window and scroll to any part of the alignment. Select {\sl File
$\Rightarrow$ Save Project} from the main menu and save in a suitable place.
-Close all windows and then load the project via the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } }
-\r\r\section{Selecting and editing sequences}
-\label{selectingandediting} \rJalview makes extensive use of selections - most of the commands available from
-its menus operate on the currently selected region of the alignment, either to
+Close all windows and then load the project {\sl via} the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } }
+
+
+\section{Selecting and editing sequences}
+\label{selectingandediting}
+Jalview makes extensive use of selections - most of the commands available from
+its menus operate on the {\sl currently selected region} of the alignment, either to
change their appearance or perform some kind of analysis. This section
illustrates how to make and use selections and groups.
-\r\subsection{Selecting parts of an alignment}
+
+\subsection{Selecting parts of an alignment}
Selections can be of arbitrary regions in an alignment, one or more complete columns, or one or more complete sequences.
-A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ New Alignment} alignment window menu options.
+A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ To New Alignment} in the alignment window menu options.
To clear (unselect) the selection press the [ESC] (escape) key.
-\subsubsection{Selecting arbitrary regions}\rTo select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press the mouse button and drag the mouse to the bottom right corner of the chosen region before releasing the mouse button. A dashed red box appears around the selected region (Figure \ref{select}). \r%[fig 12]
+\subsubsection{Selecting arbitrary regions}
+To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button. A dashed red box appears around the selected region (Figure \ref{select}).
+%[fig 12]
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{Selecting columns}\rTo select the same residues in all sequences, click and drag along the alignment ruler. This selects the entire height of the alignment. Ranges of positions can also be selected by clicking on the first position then holding down the [SHIFT] key whilst clicking the other end of the selection. Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).\r%[fig 13]
+\subsubsection{Selecting columns}
+To select the same residues in all sequences, click and drag along the alignment ruler. This selects the entire height of the alignment. Ranges of positions can also be selected by clicking on the first position then holding down the [SHIFT] key whilst clicking the other end of the selection. Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
+%[fig 13]
\begin{figure}[htbp]
\begin{center}
\label{selectrows}
\end{center}
\end{figure}
-\rTo select multiple complete sequences, click and drag the mouse down the\rsequence ID panel. The same technique as used for columns above can be used with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous ranges of sequences (Figure \ref{selectrows}).\r%[fig 14]
+
+To select multiple complete sequences, click and drag the mouse down the
+sequence ID panel. The same technique as used for columns above can be used with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous ranges of sequences (Figure \ref{selectrows}).
+%[fig 14]
\subsubsection{Making selections in Cursor mode}
-To define a selection in cursor mode (which is enabled by pressing [F2]),
-navigate to the top left corner of the proposed selection (using keystroke
-commands, the arrow keys or the mouse). Pressing the [Q] key marks this as the
+To define a selection in cursor mode (which is enabled by pressing [F2] when the alignment window is selected),
+navigate to the top left corner of the proposed selection (using the mouse, the arrow keys, or the keystroke
+commands described in Section \ref{cursormode}). Pressing the [Q] key marks this as the
corner. A red outline appears around the cursor (Figure \ref{cselect})
Navigate to the bottom right corner of the proposed selection and press the [M] key. This marks the bottom right corner of the selection. The selection can then be treated in the same way as if it had been created in normal mode.
\subsubsection{Inverting the current selection}
-The current sequence or column selection can be inverted, using {\tr Select
-$\Rightarrow$ Invert {\bf Sequence/Column} Selection} in the Alignment window.
-Inverting the selection is particularly useful when hiding regions in a large
-alignment (see Section \ref{hidecol} below). Instead of selecting the columns
-and rows that are to be hidden, simply select the region that is to be kept
-visible, and then invert the selection.\footnote{It is also possible to hide
-everything but the selected region using the {\sl View $\Rightarrow$ Hide
-$\Rightarrow$ All but selected region } menu entry.}
-\r\r\subsection{Creating groups}\rSelections are lost as soon as a different region is selected. Groups can be
+The current sequence or column selection can be inverted, using {\sl Select
+$\Rightarrow$ Invert Sequence/Column Selection} in the alignment window.
+Inverting the selection is useful when selecting large regions in an alignment,
+simply select the region that is to be kept unselected, and then invert the selection.
+This may also be useful when hiding large regions in an alignment (see Section \ref{hidingregions} below).
+Instead of selecting the columns and rows that are to be hidden, simply select the region that is to be kept
+visible, invert the selection, then select {\sl View $\Rightarrow$ Hide
+$\Rightarrow$ Selected Region }.
+
+\subsection{Creating groups}
+Selections are lost as soon as a different region is selected. Groups can be
created which are labeled regions of the alignment. To create a group, first
select the region which is to comprise the group. Then click the right mouse
button on the selection to bring up a context menu. Select {\sl Selection
\subsection{Exporting the current selection}
-The current selection can be copied to the system clipboard (in PFAM format). It can also be output to a textbox using the output functions in the pop-up menu obtained by right clicking the current selection. The textbox enables quick manual editing of the alignment prior to importing it into a new window (using the [New Window] button) or saving to a file with the {\sl File $\Rightarrow$ Save As } pulldown menu option from the text box.
+The current selection can be copied to the clipboard (in PFAM format). It can also be output to a textbox using the output functions in the pop-up menu obtained by right clicking the current selection. The textbox enables quick manual editing of the alignment prior to importing it into a new window (using the [New Window] button) or saving to a file with the {\sl File $\Rightarrow$ Save As } pulldown menu option from the text box.
\exercise{Making selections and groups}{
\label{exselect}
\exstep{Close all windows in Jalview and load the ferredoxin alignment (PFAM
ID PF03460). Choose a residue and place the mouse cursor on it. Click and drag the mouse cursor to create a selection. As you drag, a red box will `rubber band' out to show the extent of the selection. Release the mouse button and a red box should border the selected region. Now press [ESC] to clear the selection.} \exstep{
-Select one sequence by clicking on the id panel. Note that the sequence ID takes on a highlighted background and a red box appears around the selected sequence. Now hold down [SHIFT] and click another sequence ID a few positions above or below. Note how the selection expands to include all the sequences between the two positions on which you clicked.
+Select one sequence by clicking on the ID panel. Note that the sequence ID takes on a highlighted background and a red box appears around the selected sequence. Now hold down [SHIFT] and click another sequence ID a few positions above or below. Note how the selection expands to include all the sequences between the two positions on which you clicked.
Now hold down [CTRL] and click on several sequences ID's both selected and unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are individually deselected.
}
\exstep{ Repeat the step above but selecting columns by clicking on the ruler bar instead of selecting rows by clicking on the sequence ID.
}
\exstep{Press [F2] to enter Cursor mode. Navigate to column 59, row 1 by pressing {\sl 5 9 , 1 [RETURN]}. Press {\sl Q} to mark this position. Now navigate to column 65, row 8 by pressing {\sl 6 5 , 8 [RETURN]}. Press {\sl M} to complete the selection.}
\exstep{\label{exselectgrpcolour}Open the popup menu by right-clicking the
-selected region with the mouse. Open the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour } menu and select `Percentage Identity'. This will turn the selected region into a group. }
+selected region with the mouse. Open the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour } menu and select `Percentage Identity'. This will turn the selected region into a group and colour it accordingly.}
\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences by clicking on their Sequence ID label. Note how the group expands to include newly selected sequences, and the `Percentage Identity' colouring changes. }
\exstep{
Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
\exstep{
-Right click on the text area to open the selection popup-menu. Follow the menus an pick an output format from the {\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
+Right click on the text area to open the selection popup-menu. Follow the menus and pick an output format from the {\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
}
\exstep{Try manually editing the alignment and then press the [New Window] button to import the file into a new alignment window.}
% more? change colouring style. set border colour.
}
-\r\subsection{Reordering the alignment}\rSequence reordering is simple. Highlight the sequences to move then press the up or down arrow keys as appropriate (Figure \ref{reorder}). If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and then move the group rather than the individual sequence.\r\r\begin{figure}[htbp]
+
+\subsection{Reordering the alignment}
+Sequence reordering is simple. Highlight the sequences to be moved then press the up or down arrow keys as appropriate (Figure \ref{reorder}). If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and then move the group rather than the individual sequence.
+
+\begin{figure}[htbp]
\begin{center}
\includegraphics[width=3in]{images/move1.pdf}
\includegraphics[width=3in]{images/move2.pdf}
\end{figure}
\exercise{Reordering the alignment}{
-\exstep{Open an alignment (e.g.the PFAM domain PF03460). Select one sequence. Using the up and down arrow keys, alter its position in the alignment.
+\exstep{Open an alignment (e.g.the PFAM domain PF03460). Select one sequence. Using the up and down arrow keys, alter its position in the alignment. Note that this will not work in cursor mode.
}
\exstep{Hold [CTRL] and select two sequences separated by one or more un-selected sequences. Note how multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.
}
\subsection{Hiding regions}
\label{hidingregions}
-It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create several different views of the example alignment in the file that is loaded when Jalview is first started (See Figure \ref{startpage}).
+It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create the several different views in the example alignment file that is loaded when Jalview is first started (See Figure \ref{startpage}).
-To hide a set of sequences, select them and right-click the mouse on the selected sequence IDs to bring up the context menu. Select {\sl Hide Sequences} and the sequences will be concealed, with a small triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
+To hide a set of sequences, select them and right-click the mouse on the selected sequence IDs to bring up the context menu. Select {\sl Hide Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
\begin{figure}[htbp]
\includegraphics[width=1.5in]{images/hide1.pdf}
\includegraphics[width=2.5in]{images/hide2.pdf}
\includegraphics[width=1.75in]{images/hide3.pdf}
-\caption{{\bf Hiding Sequences} Hidden sequences are represented by a blue triangle in the sequence ID panel}
+\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small blue triangle in the sequence ID panel}
\label{hideseq}
\end{center}
\end{figure}
-A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns (indicated by a red marker) can be hidden and revealed in the same way via the context menu (right click) on the ruler bar. The hidden column selection is indicated by a blue triangle in the ruler bar.
+A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns (indicated by a red marker) can be hidden and revealed in the same way {\sl via} the context menu by right clicking on the ruler bar. The hidden column selection is indicated by a small blue triangle in the ruler bar.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2in]{images/hide4.pdf}
\includegraphics[width=3in]{images/hide5.pdf}
\includegraphics[width=1in]{images/hide6.pdf}
-\caption{{\bf Hiding Columns} Hidden columns are represented by a blue triangle in the ruler bar}
+\caption{{\bf Hiding Columns} Hidden columns are represented by a small blue triangle in the ruler bar}
\label{hidecol}
\end{center}
\end{figure}
It is often easier to select the region that you intend to work with, rather
-than the regions that you want to hide. In this case, use the {\sl View $\Rightarrow$ Hide
-$\Rightarrow$ All but selected region } menu entry, or press [Shift]+[Ctrl]+H
+than the regions that you want to hide. In this case, select the required region and use the {\sl View $\Rightarrow$ Hide
+$\Rightarrow$ All but Selected Region } menu entry, or press [Shift]+[Ctrl]+H
to hide the unselected region.
\subsubsection{Representing a group with a single sequence}
within a larger alignment.
\subsubsection{Undoing edits}
-Jalview supports the undoing of edits via the {\sl Edit $\Rightarrow$ Undo Edit}
+Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
{\sl Undo} function only works for edits to the alignment or sequence ordering.
\item{ If you are using OSX, and a key combination - such as [CTRL]+A - does
not work, then try pressing the [CMD] key instead of [CTRL].
}
-\item{}
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
the left so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
-O80429\_MAIZE (Hint: press [CTRL]-I to invert the sequence selection and then
+O80429\_MAIZE (Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
deselect FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they
begin at column 5 of the alignment view.}
the same way.}
\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
-insert two additional gaps after the gap at column 47: First press [Escape] to
+inserting two additional gaps after the gap at column 47: First press [ESC] to
clear the selection, then hold [SHIFT] and click and drag on the G and move it
two columns to the right.}
Select the last two sequences (FER1\_MAIZE and O80429\_MAIZE), then press [SHIFT]
and click and drag the initial methionine of O80429\_MAIZE 5 columns to the right
so it lies at column 10. Keep holding [SHIFT] and click and drag to insert
-another gap at the proline at column 25 (16P). Remove the gap at
+another gap at the proline at column 25 (25C in cursor mode). Remove the gap at
column 44, and insert 4 gaps at column 47 (after AAPM).}
\exstep{ Hold [SHIFT] and drag the I at column 39 of FER1\_MAIZE 2 columns to the
right. Remove the gap at FER1\_MAIZE column 49 by [SHIFT]+click and drag left by
-one column. Press [Escape] to clear the selection, and then insert three gaps in
+one column. Press [ESC] to clear the selection, and then insert three gaps in
FER1\_MAIZE at column 47 by holding [SHIFT] and click and drag the S in FER1\_MAIZE to the right by three columns. Finally,
remove the gap in O80429\_MAIZE at column 56 using [SHIFT]-drag to the left on
-42R.}
+56C.}
\exstep{ Use the
{\sl Edit $\Rightarrow$ Undo Edit} and {\sl Edit $\Rightarrow$ Redo Edit} menu
-option, or their keyboard shortcuts ([CTRL]+Z and [CTRL]+Y) to step backwards
-and replay the edits you have made} }
+option, or their keyboard shortcuts ([CTRL]+Z and [CTRL]+Y) to step
+backwards and replay the edits you have made.}
+
+}
\begin{figure}[htb]
\begin{center}
\includegraphics[width=3in]{images/edit1.pdf}
\includegraphics[width=3in]{images/edit2.pdf}
\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
-selected sequence is dragged to the right with [SHIFT] pressed.}
+selected sequence is dragged to the right while pressing and holding [SHIFT].}
\label{gapseq}
\end{center}
\end{figure}
\subsubsection{Editing in Cursor mode}
-Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by pressing [SPACE]. Gaps will be inserted at the cursor, pushing the residue under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE] or [SHIFT]-[SPACE] (both keys held down together).
+Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE] or [SHIFT]-[SPACE] (both keys held down together).
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. The gap under the cursor will be removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps will be deleted up to the number specified. To delete gaps from all sequences of a group, use [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down together).
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you have everything unselected by pressing ESC. The gap under the cursor will be removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps will be deleted up to the number specified. To delete gaps from all sequences of a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down together). Note that the deletion will only occur if the gaps are in the same columns in all sequences in the selected group, and those columns are to the right of the selected residue.
\exercise{Keyboard edits}{
\item{This continues on from exercise \ref{mousealedit}, and recreates the final
part of the example ferredoxin alignment from the unaligned sequences using
-Jalview's keyboard editing mode.}
+Jalview's keyboard editing mode. Note that using the [SHIFT]-[SPACE] command should have the same effect as the [CTRL]-[SPACE] command mentioned in this exercise.}
\exstep{Load the
sequence alignment at \textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the edited alignment from exercise \ref{mousealedit}. If you continue from the previous exercise, then first right click on the sequence ID panel and select {\tr Reveal All}.
%TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
\exstep{Insert 58 gaps at the start of the first sequence (FER\_CAPAA). Press {\sl 58} then {\sl [SPACE]}. }
\exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN). Hold down shift and click on the fifth (FER1\_PEA). }
-\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing {\sl 1,2} then pressing {\sl [RETURN]}. Now insert 6 gaps. Type {\sl 6} then hold down [CTRL] and press the space bar.}
-\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47. Press {\sl 3 4 C} then [CTRL]-[SPACE]. Press {\sl 3 8 C} then [CTRL]-[SPACE]. Press {\sl 4 7 C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are now aligned.}
-\exstep{The fifth sequence (FER1\_PEA) is poorly aligned. We will delete some gaps and add some new ones. Navigate to the start of sequence 5 and delete 3 gaps. Press {\sl 1 , 5 [RETURN]} then {\sl 3 [BACKSPACE]} to delete three gaps. Go to column 31 and delete the gap. Press {\sl 3 1 C [BACKSPACE]} .}
-\exstep{ Similarly delete the gap now at column 34, then insert two gaps at column 38 . Press {\sl 3 4 C [BACKSPACE] 3 8 C 2 [SPACE]}. Delete three gaps at 44 and insert one at 47 by pressing {\sl 4 4 C 3 [BACKSPACE] 4 7 C [SPACE]}. The top five sequences are now aligned.}
+\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing {\sl 1,2} then pressing {\sl [RETURN]}. Now insert 6 gaps. Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.}
+\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47. Press {\sl 34C} then
+{\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE]. Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are now aligned.}
+\exstep{The fifth sequence (FER1\_PEA) is poorly aligned. We will delete some gaps and add some new ones. Press {\sl [ESC]} to clear the selection. Navigate to the start of sequence 5 and delete 3 gaps. Press {\sl 1,5 [RETURN]} then {\sl 3 [BACKSPACE]} to delete three gaps. Go to column 31 and delete the gap. Press {\sl 31C [BACKSPACE]} .}
+\exstep{ Similarly delete the gap now at column 34, then insert two gaps at column 38. Press {\sl 34C [BACKSPACE] 38C 2 [SPACE]}. Delete three gaps at column 44 and insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are now aligned.}
}
-\r\section{Colouring sequences}
+
+\section{Colouring sequences}
\label{colours}
Colouring sequences is a key aspect of alignment presentation. Jalview allows
\subsection{Colouring the whole alignment}
-\parbox[c]{3.75in}{The alignment can be coloured via the {\sl Colour} menu option in the alignment window. Selecting the colour scheme causes all residues to be coloured. The menu is divided into three sections. The first section gives options for the behaviour of the menu options, the second lists static and dynamic colourschemes available for selection. The last gives options for making hybrid colourschemes using conservation shading or colourscheme thresholding.
+\parbox[c]{3.75in}{The alignment can be coloured {\sl via} the {\sl Colour} menu option in the alignment window. Selecting the colour scheme causes all residues to be coloured. The menu is divided into three sections. The first section gives options for the behaviour of the menu options, the second lists static and dynamic colourschemes available for selection. The last gives options for making hybrid colourschemes using conservation shading or colourscheme thresholding.
}\parbox[c]{3in}{
\centerline {
\subsection{Colouring a group or selection}
-Selections or groups can be coloured in two ways. The first is via the Alignment Window's {\sl Colour} menu, after first ensuring that the Apply to all groups flag is not selected. This must be turned off specifically as it is on by default.
+Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above, after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected. This must be turned {\sl off} specifically as it is {\sl on} by default. When unticked, selections from the Colours menu will only change the colour for residues in the current selection, or the alignment view's ''background colourscheme'' when no selection exists.
-The second method is to use the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour} context menu option obtained by right clicking on the group (Figure \ref{colgrp}).
+The second method is to use the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour} context menu option obtained by right clicking on the group (Figure \ref{colgrp}). This only changes the colour of the current selection or group.
\begin{figure}[htbp]
\begin{center}
For many colour schemes, the intensity of the colour in a column can be scaled
by the degree of amino acid property conservation. Selecting {\sl Colour
$\Rightarrow$ By Conservation} enables this mode, and {\sl Modify
-conservation threshold} brings up a selection box (the {\sl Conservation
-Threshold dialog box}) allowing the alignment colouring to be modified.
+Conservation Threshold...} brings up a selection box (the {\sl Conservation
+Colour Increment} dialog box) allowing the alignment colouring to be modified.
Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}).
\begin{figure}[htbp]
\subsubsection{ClustalX}
- \parbox[c]{3.5in}{This is an emulation of the default colourscheme used for alignments in Clustal X, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type. }
+ \parbox[c]{3.5in}{This is an emulation of the default colourscheme used for alignments in ClustalX, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type. }
\parbox[c]{3in}{\includegraphics[width=2.75in]{images/col_clustalx.pdf}}
\subsubsection{Blosum62}
-\parbox[c]{3.5in}{Gaps are coloured white. If a residue matches the consensus sequence residue at that position it is coloured dark blue. If it does not match the consensus residue but the Blosum 62 matrix gives a positive score, it is coloured light blue.}
+\parbox[c]{3.5in}{Gaps are coloured white. If a residue matches the consensus sequence residue at that position it is coloured dark blue. If it does not match the consensus residue but the Blosum62 matrix gives a positive score, it is coloured light blue.}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_blosum62.pdf}
}
}
\subsubsection{User Defined}
-This dialogue allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu
+This dialogue allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu (Figure \ref{usercol}).
\begin{figure}[htbp]
\includegraphics[width=2.5in]{images/col_user1.pdf}
\includegraphics[width=2in]{images/col_user2.pdf}
\includegraphics[width=1.75in]{images/col_user3.pdf}
-\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed via the {\sl Colour} menu (right).}
+\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
\label{usercol}
\end{center}
\end{figure}
}
\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.
}
-\exstep{ Insert a name in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.
+\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.
}
\exstep{
The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
}
}
-\r\section{Alignment formatting and graphics output}
+
+\section{Alignment formatting and graphics output}
\label{layoutandoutput}
Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output, the layout that is seen on screen will be the same as what is output in an exported graphics file. It is therefore important to pick the right kind of display layout prior to generating figures.
Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\tr Views}. Because each view displays the same underlying data, any edits performed in one view will update the alignment or annotation visible in all views.
-\parbox[c]{4in}{Alignment views are created using the {\tr View $\Rightarrow$ New View} option of the alignment window. This will create a new view with the same groups, alignment layout and display options as the current one. Views may be gathered (by pressing G) together as named tabs on the alignment window, or displayed simultaneously in their own window (by pressing X).}\parbox[c]{2.75in}{
+\parbox[c]{4in}{Alignment views are created using the {\sl View $\Rightarrow$ New View} option of the alignment window or by Pressing [CTRL]-T. This will create a new view with the same groups, alignment layout and display options as the current one. Pressing G will gather together Views as named tabs on the alignment window, and pressing X will expand gathered Views so they can be viewed simultaneously in their own separate windows. To delete a group, press [CTRL]-W.}\parbox[c]{2.75in}{
\begin{center}\centerline{
\includegraphics[width=2.5in]{images/mulv_tabs.pdf}}
\end{center}
\subsection{Alignment layout}
Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped, where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
+
\subsubsection{Wrapped alignments}
-Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation lines are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when working with large numbers of sequences. Furthermore, alignment annotation (see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult.
+Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation lines are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when working with large numbers of sequences.
+
+If annotations are not all visible in wrapped mode, expand the alignment window to view them. Note that alignment annotation (see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult.
\begin{figure}[htbp]
\begin{center}
\parbox[c]{2in}{\includegraphics[width=2in]{images/wrap1.pdf}}
\subsubsection{Fonts}
-\parbox[c]{4in}{The text appearance in a view can be modified via the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
+\parbox[c]{4in}{The text appearance in a view can be modified {\sl via} the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
\parbox[c]{2in}{\centerline{\includegraphics[width=1.75in]{images/font.pdf}}}
\subsubsection{Numbering and label justification}
-Options in the {\sl Format} menu are provided to control the also provides a range of options to control the display of sequence and alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
+Options in the {\sl Format} menu are provided to control the alignment view, and provide a range of options to control the display of sequence and alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
\subsubsection{Alignment and Group colouring and appearance}
The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Hidden Markers} and {\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.
\subsubsection{Highlighting nonconserved symbols}
The alignment layout and group sub-menu both contain an option to hide
conserved symbols from the alignment display ({\sl Format $\Rightarrow$ Show
-nonconserved } in the alignment window or {\sl Popup Menu $\Rightarrow$ Group
-$\Rightarrow$ Show nonconserved}). This mode is useful when working with
+nonconserved } in the alignment window or {\sl Selection $\Rightarrow$ Group
+$\Rightarrow$ Show Nonconserved} by right clicking on a group). This mode is useful when working with
alignments that exhibit a high degree of homology, because Jalview will only
display gaps or sequence symbols that differ from the consensus for each
column, and render all others with a `.'.
% TODO: describe consensus, conservation, quality user preferences, and group
% annotation preferences.
The annotation lines which appear below the sequence alignment are described in
-detail in Section \ref{annot}. They can be hidden by toggling the {\sl View
+detail in Section \ref{featannot}. They can be hidden by toggling the {\sl View
$\Rightarrow$ Show Annotations} menu option. Additionally, each annotation line
-can be hidden and revealed in the same way as sequences via the context menu on
+can be hidden and revealed in the same way as sequences {\sl via} the context menu on
the annotation name panel (Figure \ref{annot}). Annotations can be reordered by
dragging the annotation line label on the annotation label panel. Placing the
-mouse over the top annotation label brings up a resize icon. When this is
-displayed, Click-dragging up and down alters the relative size of the sequence
-alignment and annotation alignment panels.
+mouse over the top annotation label brings up a resize icon on the left. When this is
+displayed, Click-dragging up and down provides more space in the alignment window for viewing the annotations, and less space for the sequence alignment.
\begin{figure}
\begin{center}
\subsection{Graphical output}
\label{figuregen}
-\parbox[c]{4in}{Jalview allows alignments figures to be exported in three different formats, each of which is suited to a particular purpose. Image export is via the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ \ldots } alignment window menu option. }
+\parbox[c]{4in}{Jalview allows alignments figures to be exported in three different formats, each of which is suited to a particular purpose. Image export is {\sl via} the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ \ldots } alignment window menu option. }
\parbox[c]{2in}{\centerline{\includegraphics[width=1.25in]{images/image.pdf}}}
\subsubsection{HTML}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_html.pdf}}}
\subsubsection{EPS}
-\parbox[c]{3in}{EPS is Encapsulated Postscript. It is the format of choice for publication and posters as it gives the highest quality output of any of the image types. It can be scaled indefinitely so will still look good on an A0 poster. This format can be read by most good presentation and graphics packages such as Adobe Illustrator.
+\parbox[c]{3in}{EPS is Encapsulated Postscript. {\bf It is the format of choice
+for publications and posters} as it gives the highest quality output of any of
+the image types. It can be scaled to any size, so will still look good on an A0
+poster.
+This format can be read by most good presentation and graphics packages such as Adobe Illustrator or Inkscape.
}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_eps.pdf}} \par \centerline{Zoom Detail of EPS image.}}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
\exercise{Graphical Output}{
\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}. Customise it how you wish but leave it unwrapped. Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu. Save the file and open it in your favourite web browser. }
-\exstep{Now wrap the alignment (Exercise \ref{exscreen}) and export the image to HTML again. Compare the two images. Note that the exported image matches the format displayed in the alignment window but annotations are not exported.}
-\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option. Open the file in an image viewer that allows zooming (eg. Paint or Photoshop on Windows, Preview on Mac OS X) and zoom in. Notice that the image is a bitmap and it becomes pixelated very quickly. Note also that the annotation lines are included in the image.}
-\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ EPS} menu option. Open the file in a suitable program such as Ghostview or Preview (Mac OS X). Zoom in and note that the image is indefinitely scalable.}
-}
+\exstep{Now wrap the alignment and export the image to HTML again. Compare the two images. Note that the exported image matches the format displayed in the alignment window but {\bf annotations are not exported}.}
+\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option. Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in. Notice that the image is a bitmap and it becomes pixelated very quickly. Note also that the {\bf annotation lines are included} in the image.}
+\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image
+$\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
+Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
+Preview (Mac OS X). Zoom in and note that the image has near-infinite
+resolution.} }
\chapter{Analysis and Annotation}
\label{analysisannotation}
-This chapter describes the annotation, analysis, and visualization tasks that the Jalview Desktop can perform. Section \ref{wkwithstructure} introduces the structure visualization capabilities of Jalview. In Section \ref{alignanalysis}, you will find details of the Tree building, viewing and PCA capabilities, alignment redundancy removal, pairwise alignments and alignment conservation analysis. Subsequently, in Section \ref{jvwebservices}, programs available remotely for multiple sequence alignment and secondary structure prediction are described.
+This chapter describes the annotation, analysis, and visualization tasks that
+the Jalview Desktop can perform. Section \ref{wkwithstructure} introduces the
+structure visualization capabilities of Jalview. In Section \ref{alignanalysis},
+you will find details of the Tree building, viewing and PCA capabilities,
+alignment redundancy removal, pairwise alignments and alignment conservation
+analysis. Section \ref{jvwebservices} introduces the various web based services
+available to Jalview users, and Section \ref{msaservices}
+describes how to use the range of multiple alignment programs provided by JABA
+(see Section \ref{jabaservices}). Similarly, Section \ref{protsspredservices}
+explains how to perform protein secondary structure predictions with JPred.
Section \ref{featannot} describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation and how they are displayed, imported and exported. Section \ref{featuresfromdb} discusses the retrieval of database references and establishment of sequence coordinate systems for the retrieval and display of features from databases and DAS annotation services. Finally, Section \ref{workingwithnuc} describes functions and visualization techniques relevant to working with nucleotide sequences, coding region annotation and nucleotide sequence alignments.
\subsection{Automatic association of PDB structures with sequences}
Jalview can automatically determine which structures are associated with a
sequence in a number of ways.
-\subsubsection{Discovery of PDB ids from sequence database cross-references}
-if a sequence has an ID from a public database that contains cross-references to
-the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl $<$Sequence ID$>$ $\Rightarrow$ Structure $\Rightarrow$
-Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (where {\sl $<$Sequence ID$>$} is the ID of the sequence on which
-you clicked) (Figure \ref{auto}). Jalview will attempt to associate the
+\subsubsection{Discovery of PDB IDs from sequence database cross-references}
+If a sequence has an ID from a public database that contains cross-references to
+the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl Structure $\Rightarrow$
+Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (Figure \ref{auto}). Jalview will attempt to associate the
sequence with a Uniprot sequence and from there discover any associated PDB
structures. This takes a few seconds and applies to all sequences in the
alignment which have valid Uniprot IDs. On moving the cursor over the sequence
\subsubsection{Drag-and-drop association of PDB files with sequences by filename
match}
\label{multipdbfileassoc}
-If one or more PDB files are dragged from a file browser onto an alignment
-window, Jalview will search the alignment for sequences with IDs that
-matches any of the files dropped onto the alignment. If it discovers matches, a
+If one or more PDB files stored on your computer are dragged from their location on the file browser
+onto an alignment window, Jalview will search the alignment for sequences with IDs that
+match any of the files dropped onto the alignment. If it discovers matches, a
dialog like the one in Figure \ref{multipdbfileassocfig} is shown, giving the
option of creating associations for the matches.
If no associations are made, then sequences extracted
-from the structure will be simply appended to the alignment. However, if only
-some of the files are associated, jalview will raise another dialog box giving
-you the option to add any remaining sequences the structure files not present in
+from the structure will be simply added to the alignment. However, if only
+some of the PDB files are associated, jalview will raise another dialog box giving
+you the option to add any remaining sequences from the PDB structure files not present in
the alignment. This allows you to easily decorate sequences in a newly imported
-alignment with any corresponding structures you've collected in a directory
+alignment with any corresponding structures you've already collected in a directory
accessible from your computer.\footnote{We plan to extend this facility in
future so Jalview will automatically search for PDB files matching your
sequence within a local directory. Check out
\href{http://issues.jalview.org/browse/JAL-801}{Jalview issue 801}}
+% there is no mention of the other footnote (#3) that appears saying: Tip: The sequence ID tooltip can often become large for heavily cross-referenced sequence IDs. Use the ...
+% JBP: yes there is - under 'Discovery of ' subsection.
\begin{figure}[htbp]
\begin{center}
\includegraphics[]{images/pdbdragdropassoc.pdf}
\caption{{\bf Associating PDB files with sequences by drag-and-drop.} Dragging
-PDB files to an alignment of sequences with names matching the dragged
+PDB files onto an alignment of sequences with names matching the dragged
files names (A), results in a dialog box (B) that gives the option to associate each file with any sequences with matching IDs. }
\label{multipdbfileassocfig}
\end{center}
the local file system, and shown as a ribbon diagram coloured according to the
associated sequence in the current alignment view (Figure \ref{structure}
(right)). The structure can be rotated by clicking and dragging in the structure
-window. The structure can be zoomed using the mouse scroll wheel (if available).
+window. The structure can be zoomed using the mouse scroll wheel or by [SHIFT]-dragging the structure.
Moving the mouse cursor over a sequence to which the structure is linked in the
-alignment panel highlights the respective residue's sidechain atoms. The
+alignment view highlights the respective residue's sidechain atoms. The
sidechain highlight may be obscured by other parts of the molecule. Similarly,
moving the cursor over the structure shows a tooltip and highlights the
-corresponding residue in the alignment. Often, the position highlighted may not
+corresponding residue in the alignment. Clicking the alpha carbon toggles the highlight
+and residue label on and off. Often, the position highlighted in the sequence may not
be in the visible portion of the current alignment view. If the alignment
-window's {\sl View $\Rightarrow$ Automatic Scrolling } option is not selected,
-then you may have to manually move the alignment scroll bars to see the
+window's {\sl View $\Rightarrow$ Automatic Scrolling } option is selected, however,
+then Jalview will automatically move the alignment scroll bars to show the
highlighted region.
\begin{figure}[htbp]
associated sequence(s) in the alignment view from which it was launched. The
structure can be coloured independently of the sequence by selecting an
appropriate colour scheme from the {\sl Colours} menu. It can be coloured
-according to the alignment using the {\sl Colours $\Rightarrow$ By Sequence } option. The image in the structure viewer can be
-output to EPS or PNG format via the {\sl File $\Rightarrow$ Save As
-$\Rightarrow$ \ldots} submenu. The mapping between the structure and the
+according to the alignment using the {\sl Colours $\Rightarrow$ By Sequence } option. The image in the structure viewer can be saved as an EPS or PNG with the {\sl File $\Rightarrow$ Save As
+$\Rightarrow$ \ldots} submenu, which also allows the raw data to be saved as PDB format. The mapping between the structure and the
sequence (How well and which parts of the structure relate to the sequence)
can be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up
the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
Associate Structure with Sequence $\Rightarrow$ Discover
-PDB ids}. Jalview will now attempt to find PDB structures for the sequences in
+PDB IDs}. Jalview will now attempt to find PDB structures for the sequences in
the alignment. } \exstep{ Right-click on the sequence ID for {\sl FER1\_SPIOL}.
Select { \sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$ View Structure
-$\Rightarrow$ 1A70} A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel. } \exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. } \exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press {\sl OK} to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with your web browser. }
+$\Rightarrow$ 1A70}. A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel. } \exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
+\exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press OK to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with a suitable program. }
\exstep{Select {\sl File $\Rightarrow$ View Mapping} from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.}
-
\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file. Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
-\exstep{Right click on the structure to bring up the Jmol window. Explore the menu options. Try to change the style of molecular display - by first using the {\sl Jmol $\Rightarrow$ Select $\Rightarrow$ all} command, and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and stick} command.}
+\exstep{Right click on the structure to bring up the Jmol window. Explore the menu options. Try to change the style of molecular display - by first using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.}
\exstep{Use the {\sl File $\Rightarrow$ Save As .. } function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
Verify that the Jmol display is as it was when you just saved the file.}
structures.
\subsubsection{Obtaining the RMSD for a superposition}
-Figure \ref{mstrucsuperposition} shows a superposition created during the course
+The RMSD (Root Mean Square Deviation) is a measure of how similar the structures are when they are superimposed. Figure \ref{mstrucsuperposition} shows a superposition created during the course
of Exercise \ref{superpositionex}. The parts of each molecule used to construct
the superposition are rendered using the cartoon style, with other parts of
the molecule drawn in wireframe. The Jmol console, which has been opened after
the superposition was performed, shows the RMSD report for the superposition.
Full information about the superposition is also output to the Jalview console,
-including the precise atom pairs used to superpose structures.
+including the precise atom pairs used to superpose structures.
\subsubsection{Choosing which part of the alignment is used for structural
superposition}
Jalview uses the visible part of each alignment view to define which parts of
-each molecule are to be corresponded. Hiding a column in a view used for
-superposition will remove that correspondence from the set, allowing
-the selection of specific parts of the alignment to be used for
+each molecule are to be superimposed. Hiding a column in a view used for
+superposition will remove that correspondence from the set, and will exclude it from the superposition and RMSD calculation.
+This allows the selection of specific parts of the alignment to be used for
superposition. Only columns that define a complete set of correspondences for
all structures will be used for structural superposition, and as a consequence,
the RMSD values generated for each pair of structures superimposed can be
directly compared.
In order to recompute a superposition after changing a view or editing the
-alignment, select the {\sl Jmol $\Rightarrow$ Align } menu option. The {\sl
+alignment, select the {\sl Jmol $\Rightarrow$ Align sequences } menu option. The {\sl
Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
associated alignments and views are to be used to create the set of
correspondences. This menu is useful when composing complex superpositions
involving multi-domain and multi-chain complexes, when correspondences may be
defined by more than one alignment.
+Note that these menu options appear when you have two or more structures in one Jmol viewer.
+
+
\begin{figure}[htbp]
\begin{center}
the small section and with the whole alignment. Which view do you think give the
best 3D superposition, and why ?} }
-\subsection{Colouring structure data associated with multiple alignments and
-views}
+\subsection{Colouring structure data associated with multiple alignments and views}
Normally, the original view from which a particular structure view was
opened will be the one used to colour structure data. If alignments involving
sequences associated with structure data shown in a Jmol have multiple views, Jalview gives you full control
over which alignment, or alignment view, is used to colour the structure
display. Sequence-structure colouring associations are
-changed {\sl via} the {\sl View $\Rightarrow$ Colour by} menu, which lists all
+changed {\sl via} the {\sl View $\Rightarrow$ Colour by ..} menu, which lists all
views associated with data shown in the embedded Jmol view. A tick is shown beside
views currently used as colouring source, and moving the
mouse over each view will bring it to the front of the alignment display,
allowing you to browse available colour sources prior to selecting one. If the
{\sl Select many views} option is selected, then multiple views can be selected as sources for colouring the
-structure data. {\sl Invert selection} and {\sl Select all} options are also provided to quickly change between multi-view selections.
+structure data. {\sl Invert selection} and {\sl Select all views} options are also provided to quickly change between multi-view selections.
+
+Note that the {\sl Select many views} option is useful if you have different
+views that colour different areas or domains of the alignment. This option is
+further explored in Section \ref{complexstructurecolours}.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5.5in]{images/mviewstructurecol.pdf}
\caption{{\bf Choosing a different view for colouring a structure display}
Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control
-of which alignment view is used to colour structures when the {\sl Colour
-$\Rightarrow$ Colour by sequence} option is selected.}
+of which alignment view is used to colour structures when the {\sl Colours
+$\Rightarrow$ By Sequence} option is selected.}
\label{mviewstructurecol}
\end{center}
\end{figure}
\subsubsection{Colouring complexes}
-
-The ability to control which multiple alignment or view is used to colour
+\label{complexstructurecolours}
+The ability to control which multiple alignment view is used to colour
structural data is essential when working with data relating to
multidomain biomolecules and complexes.
structure view. An example of this is shown in Figure
\ref{mviewalcomplex}, based on data from Song et. al\footnote{Structure of
DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Jikui Song, Olga Rechkoblit, Timothy H. Bestor, and Dinshaw J. Patel.
-{\sl Science} {\bf 331} 1036-1040
+{\sl Science} 2011 {\bf 331} 1036-1040
\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
\begin{figure}[htbp]
step 1 onto one of the alignments to associate it with the mouse sequence in
that Pfam domain family.}
\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
-ID popup menu's structure submenu to view the DNMT1\_MOUSE structure for the associated mouse sequence. Check the contents of
-the {\sl View $\Rightarrow$ Colour by ..} submenu to see what alignments can be used to
+ID popup menu's {\sl Structure} submenu to view the DNMT1\_MOUSE structure for the associated mouse sequence. When given the option, {\bf view all of the structures in the same Jmol viewer}. Check the contents of the {\sl View $\Rightarrow$ Colour by ..} submenu to see what alignments can be used to
colour the sequence.}
\exstep{Repeat the previous two steps for each of
the other alignments. In each case, when performing the `View DNMT1\_MOUSE.pdb'
-step, Jalview will ask you if you wish to create a new Jmol view. You should
-respond `No', ensuring that each sequence fragment is associated with the same Jmol view.}
+step, Jalview will ask if you wish to create a new Jmol view. You should
+respond `No', {\bf ensuring that each sequence fragment is associated with the same Jmol view}.}
\exstep{Pick a different colourscheme for each alignment, and use the {\sl
Colour by ..} submenu to ensure they are all used to colour the complex shown
in the Jmol window.}
{\bf Conservation} annotation row. This function was described in section
\ref{colourbyannotation}.
+Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu option, or you may not see any colour changes in the associated structure.
+
{\sl Note: Choose a different shading scheme for each
alignment so that the regions of strong physicochemical conservation are highlighted. This
kind of shading will reveal conserved regions of interaction between domains
\section{Analysis of alignments}
\label{alignanalysis}
-Jalview provides support for sequence analysis in two ways. A number of analytical methods are `built-in' and run inside Jalview itself and are mostly accessed from the {\sl Calculate} alignment window menu. Computationally intensive analyses are run outside Jalview via web services - these are typically accessed via the {\sl Web Services} menu, and described in Section \ref{jvwebservices}. In this section, we describe the built-in analysis capabilities common to both the Jalview Desktop and the JalviewLite applet.
+Jalview provides support for sequence analysis in two ways. A number of analytical methods are `built-in', these are accessed from the {\sl Calculate} alignment window menu. Computationally intensive analyses are run outside Jalview {\sl via} web services - these are typically accessed {\sl via} the {\sl Web Service} menu, and described in \ref{jvwebservices} and subsequent sections. In this section, we describe the built-in analysis capabilities common to both the Jalview Desktop and the JalviewLite applet.
\subsection{PCA}
This calculation creates a spatial representation of the similarities within the current selection or the whole alignment if no selection has been made. After the calculation finishes, a 3D viewer displays the each sequence as a point in 3D `similarity space'. Sets of similar sequences tend to lie near each other in this space.
-Note: The calculation is computationally expensive, and may fail for very large sets of sequences - because the JVM has run out of memory. Memory issues were discussed in Section \ref{memorylimits}.
+Note: The calculation is computationally expensive, and may fail for very large sets of sequences - because the JVM has run out of memory. Memory issues, and how to overcome them, were discussed in Section \ref{memorylimits}.
\subsubsection{What is PCA?}
Principal components analysis is a technique for examining the structure of complex data sets. The components are a set of dimensions formed from the measured values in the data set, and the principle component is the one with the greatest magnitude, or length. The sets of measurements that differ the most should lie at either end of this principle axis, and the other axes correspond to less extreme patterns of variation in the data set.
-In this case, the components are generated by an eigenvector decomposition of the matrix formed from the sum of BLOSUM scores at each aligned position between each pair of sequences. The basic method is described in the 1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl Nature Structural Biology} (1995) {\bf 2}, 171-8. \rPMID: 7749921} and implemented at the SeqSpace server at the EBI.
+In this case, the components are generated by an eigenvector decomposition of the matrix formed from the sum of BLOSUM scores at each aligned position between each pair of sequences. The basic method is described in the 1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl Nature Structural Biology} (1995) {\bf 2}, 171-8.
+PMID: 7749921} and implemented at the SeqSpace server at the EBI.
\subsubsection{The PCA Viewer}
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle Component Analysis} menu option. PCA requires a selection containing at least 4 sequences. A window opens containing the PCA tool (Figure \ref{PCA}). Each sequence is represented by a square, coloured by the background colour of the sequence ID label. The axes can be rotated by clicking and dragging the left mouse button and zoomed using the $\uparrow$ and $\downarrow$ keys or the scroll wheel of the mouse (if available). A tool tip appears if the cursor is placed over a sequence. Sequences can be selected by clicking on them. [CTRL]-Click can be used to select multiple sequences.
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle Component Analysis} menu option. {\bf PCA requires a selection containing at least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}). Each sequence is represented by a small square, coloured by the background colour of the sequence ID label. The axes can be rotated by clicking and dragging the left mouse button and zoomed using the $\uparrow$ and $\downarrow$ keys or the scroll wheel of the mouse (if available). A tool tip appears if the cursor is placed over a sequence. Sequences can be selected by clicking on them. [CTRL]-Click can be used to select multiple sequences.
\begin{figure}[hbtp]
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\label{PCA}
\end{center}
\end{figure}
-Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$ Show Labels} menu option, and the plot background colour changed via the {\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical representation of the PCA plot can be exported as an EPS or PNG image via the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
+Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$ Show Labels} menu option, and the plot background colour changed {\sl via} the {\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical representation of the PCA plot can be exported as an EPS or PNG image {\sl via} the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
\exercise{Principle Component Analysis}{
\exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar} and select {\sl Select
-$\Rightarrow$ Undefine Groups}. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
+\textsf{http://www.jalview.org/examples/exampleFile.jar} and press [ESC] to clear any selections. Alternatively, select {\sl Select $\Rightarrow$ Undefine Groups} to remove all groups and colourschemes. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
\exstep{
Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups, each of a different colour. Note how the colour of the sequence ID label matches both the colour of the partitioned tree and the points in the PCA plot.
}
\subsection{Trees}
\label{trees}
-Jalview can calculate and display trees, providing interactive tree-based grouping of sequences though a tree viewer. All trees are calculated via the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu. Trees can be calculated from distance matrices determined from \% identity or aggregate BLOSUM 62 score using either average distance (UPGMA) or Neighbour joining algorithms. The input data for a tree calculation is either the visible portions of the current selection, or the whole alignment if no selection is present.
+Jalview can calculate and display trees, providing interactive tree-based grouping of sequences though a tree viewer. All trees are calculated {\sl via} the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu. Trees can be calculated from distance matrices determined from \% identity or aggregate BLOSUM 62 score using either {\sl Average Distance} (UPGMA) or {\sl Neighbour Joining} algorithms. The input data for a tree is either the selected region or the whole alignment, excluding any hidden regions.
On calculating a tree, a new window opens (Figure \ref{trees1}) which contains
the tree. Various display settings can be found in the tree window {\sl View}
menu, including font, scaling and label display options, and the {\sl File
$\Rightarrow$ Save As} submenu contains options for image and Newick file
export. Newick format is a standard file format for trees which allows them to
-be exported to other programs. Jalview can also read in external trees in Newick format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf names on imported trees will be matched to the associated alignment - unmatched
+be exported to other programs. Jalview can also read in external trees in Newick format {\sl via} the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf names on imported trees will be matched to the associated alignment - unmatched
leaves will still be displayed, and can be highlighted using the {\sl View
-$\Rightarrow$ Show Unlinked Leaves} menu option.
+$\Rightarrow$ Mark Unlinked Leaves} menu option.
\begin{figure}
\end{figure}
-Clicking on the tree brings up a cursor across the height of the tree. The sequences are automatically partitioned and coloured (Figure \ref{trees2}). To group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order} alignment window menu option and the correct tree. The sequences will then be sorted according to the leaf order currently shown in the tree view. The coloured background to the sequence IDs can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the alignment window menu.
+Clicking on the tree brings up a cursor across the height of the tree. The
+sequences are automatically partitioned and coloured (Figure \ref{trees2}). To
+group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
+By Tree Order $\Rightarrow$ \ldots} alignment window menu option and choose the
+correct tree. The sequences will then be sorted according to the leaf order currently shown in the tree view. The coloured background to the sequence IDs can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the alignment window menu. Note that tree partitioning will also remove any groups and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to preserve these.
\begin{figure}
\begin{center}
\subsubsection{Changing the associated view for a tree or PCA viewer}
\parbox[c]{4in}{
-The {\sl View $\Rightarrow$ Associated View $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display in accord with the colouring and selection state of the newly associated view.
+The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display according to the colouring and selection state of the newly associated view.
} \parbox[c]{3in}{\centerline{
\includegraphics[width=2.5in]{images/pca_vmenu.pdf} }}
\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the diferences between the two trees, calculated using different methods.}
\exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
-Comparing the location of individual sequences between the two trees illustrates the importance of selecting appropriate regions of the alignment for the calculation of trees.
+Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the alignment for the calculation of trees.
}
-\exstep{Recover the input data for the tree you just calculated. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is not ticked, and insert one gap in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
+\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
-A warning dialog box {\bf ``Sequences must be aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
+A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
\exstep{Now select {\sl Edit $\Rightarrow$ Pad Gaps } and try to perform the tree calculation again - this time a new tree should appear.
\label{treeconsanaly}
Trees reflect the pattern of global sequence similarity exhibited by the
-alignment or region within the alignment that was used for their calculation.
+alignment, or region within the alignment, that was used for their calculation.
The Jalview tree viewer enables sequences to be partitioned into groups based
-on the tree, by clicking within the tree viewer window. Once subdivided, the
+on the tree. This is done by clicking within the tree viewer window. Once subdivided, the
conservation between and within groups can be visually compared in order to
-better understand the pattern of similarity revealed by the tree, and the
+better understand the pattern of similarity revealed by the tree and the
variation within the clades partitioned by the grouping. The conservation based
colourschemes and the group associated conservation and consensus annotation
-(enabled using the alignment window's {\sl View $\Rightarrow$ Automatic
-Annotation $\Rightarrow$ Group Consensus} and {\sl Group Conservation} options)
+(enabled using the alignment window's {\sl View $\Rightarrow$ Autocalculated
+Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
can help when working with larger alignments.
\exercise{Tree Based Conservation Analysis}{
\label{consanalyexerc}
-\exstep{Load the PF03460 Seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the sort submenu to order alignment using the calculated tree.}
+\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
+\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the {\sl Sort Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.}
\exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
-You may find it easier to browse the alignment by if you uncheck the {\sl Show Annotations} view option, and open the overview window to aid navigation.}
+You may find it easier to browse the alignment if you first uncheck the {\sl View $\Rightarrow$ Show Annotations} option, and open the Overview Window to aid navigation.}
\exstep{Try changing the colourscheme to BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected)}
{\sl Note: You may want to save the alignment and tree as a project file, since
it is used in the next few exercises. } }
\subsection{Redundancy Removal}
-The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented, rather than deleted.}.
+The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented by a chosen sequence, rather than deleted.}.
\begin{figure}
\begin{center}
\includegraphics[width=5.5in]{images/redundancy.pdf}
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% similar under this alignment.}
-\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Show Linked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
+\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
\exstep{Use the [Undo] button on the dialog to recover the sequences. Note that the * symbols disappear from the tree display.}
\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
}
These annotations can be hidden and deleted but are only created on loading an
alignment. If they are deleted then the alignment should be saved and reloaded
to restore them. Jalview provides a toggle to autocalculate a consensus
-sequence upon editing. This is normally left selected but for large alignments
-can be turned off via the {\sl Calculate $\Rightarrow$ Autocalculate
-Consensus} menu option if the interface is too sluggish.
+sequence upon editing. This is normally selected by default, but can be turned off for large alignments
+{\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
+Consensus} menu option if the interface is too slow.
\subsubsection{Group Associated Annotation}
\label{groupassocannotation}
Group associated consensus and conservation annotation rows reflect the
sequence variation within a particular group. Their calculation is enabled
by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
-the {\sl View $\Rightarrow$ Automatic Annotation } submenu of the alignment
+the {\sl View $\Rightarrow$ Autocalculated Annotation } submenu of the alignment
window.
\subsubsection{Alignment and Group Sequence Logos}
The consensus annotation row that is shown below the alignment can be overlaid
with a sequence logo that reflects the symbol distribution at each column of
-the alignment. Right click on the Consensus annotation row and select the `Show
-Logo' option to display the Consensus profile for the group or alignment.
+the alignment. Right click on the Consensus annotation row and select the {\sl Show
+Logo} option to display the Consensus profile for the group or alignment.
Sequence logos can be enabled by default for all new alignments {\sl via} the
Visual tab in the Jalview desktop's preferences dialog box.
\exercise{Group conservation analysis}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc})} \exstep{Create a new view, and ensure the annotation panel is displayed, and
-enable the display of {\sl Group Consensus}, and the display of sequence
+enable the display of {\sl Group Consensus} and the display of sequence
logos to make it easier to see the different residue populations within each group.}
\exstep{Select a column exhibiting about 50\% conservation that lies within the
central conserved region of the alignment. Subdivide the alignment according to
{\sl Hint: You may need to hide the intervening columns
before you can select both of the columns that you wish to use to subdivide
the alignment.}}
-\exstep{Switch back to the original view, and experiment with subdividing the tree groups made in the previous excercise.}
+\exstep{Switch back to the original view, and experiment with subdividing the tree groups made in the previous exercise.}
}
\subsection{Other Calculations}
\subsubsection{Pairwise Alignments}
-Jalview can calculate optimal pairwise alignments between arbitrary sequences via the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option. Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
+Jalview can calculate optimal pairwise alignments between arbitrary sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option. Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
\begin{figure}[]
\begin{center}
a range of bioinformatics analysis tasks. }
\parbox[c]{1.75in}{\includegraphics[width=1.65in]{images/wsmenu.pdf}}
-\subsection{One way web services}
+\subsection{One-way web services}
There are three types of one way service in jalview. Database services,
which were introduced in in Section \ref{fetchseq}, provide sequence and
Links} submenu of the sequence ID popup menu. These are configured
in the {\sl Connections} tab of the {\sl Preferences} dialog box.
-The Envision2 services presented in the webservice menu provides are the first
-example of one way services where multiple sequences or sequence IDs can be
-sent. The {\sl Web services $\Rightarrow$ Envision2 Services} menu entry
+The Envision 2 services presented in the webservice menu provides are the first
+example of one-way services where multiple sequences or sequence IDs can be
+sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
provides two sub-menus that enable you to submit the sequences or IDs
associated with the alignment or just the currently selected sequences to one
of the Envision2 workflows. Selecting any one will open a new browser window on
Project Files\footnote{This may be rectified in future versions.}, so it is
important that you do not close Jalview whilst a job is running. It is also
essential that you have a continuous network connection in order to
-successfully use Web Services from Jalview, since it periodically checks the
+successfully use web services from Jalview, since it periodically checks the
progress of running jobs.
\subsection{JABA Web Services for sequence alignment and analysis}
-JABA stands for ÔJAva Bioinformatics AnalysisÕ, which is a system developed by
-Peter Troshin and Geoff Barton at the University of Dundee for running
+\label{jabaservices}
+JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
+by Peter Troshin and Geoff Barton at the University of Dundee for running
computationally intensive bioinformatics analysis programs. A JABA installation
typically provides a range of JABA web services (JABAWS) for use by other
-programs, like Jalview.
+programs, such as Jalview.
Exercises in the remainder of this section will demonstrate the simplest way of
installing JABA on your computer, and configuring Jalview so it can access the JABA services. If you
\subsection{Changing the Web Services menu layout}
\label{changewsmenulayout}
If you are working with a lot of different JABA services, you may wish to
-change the way Jalview lays out the web services menu. You can do this from the Web Services tab of the Preferences dialog box.
+change the way Jalview lays out the web services menu. You can do this from the Web Services tab of the {\sl Preferences} dialog box.
\exercise{Changing the Layout of the Web Services Menu}{
\label{changewsmenulayoutex}
\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment windowÕs Web Services menu.}
+current layout of the alignment window�s {\sl Web Service} menu.}
\exstep{Open the preferences dialog box and select the web services tab.}
-\exstep{Ensure the ÔEnable JABAWS servicesÕ checkbox is selected, and unselect
-the ÔEnable Enfin ServicesÕ checkboxes.}
-\exstep{Hit ÔRefresh servicesÕ to update the web service menu -- once the
-progress bar has completed, open the web services menu to view the changes.}
-\exstep{Unselect the ÔIndex by hostÕ checkbox and refresh the services once again.
+\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
+the {\sl Enable Enfin Services} checkboxes.}
+\exstep{Hit {\sl Refresh Services} to update the web services menu -- once the
+progress bar has completed, open the {\sl Web Service} menu to view the changes.}
+\exstep{Select the {\sl Index by host} checkbox and refresh the services once again.
{\sl Observe the way the layout of the JABAWS Alignment submenu changes.}
}
-\exstep{Do the same with the ÔIndex by typeÕ checkbox.}
+\exstep{Do the same with the {\sl Index by type} checkbox.}
}
-Jalview provides these options for configuring the layout of the web services
+Jalview provides these options for configuring the layout of the {\sl Web Service}
menu because different Jalview users may have access to a different number of
JABA services, and each will have their own preference regarding the layout of
the menu.
\end{figure}
\subsection{Running your own JABA server}
-You can download and run JABA on your own machine using the ÔVMWareÕ or
+You can download and run JABA on your own machine using the `VMWare' or
VirtualBox virtual machine environments. If you would like to learn how to do
this, there are full instructions at the
\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
}
\exstep{If you do not have VMWare player installed, download it from
-www.vmware.com (this takes a few minutes Ð you will need to register and wait
+www.vmware.com (this takes a few minutes -- you will need to register and wait
for an email with a download link).}
-\exstep{Download the JABA virtual appliance archive called Ôjaba-vm.zipÕ from
+\exstep{Download the JABA virtual appliance archive called `jaba-vm.zip' from
\textsf{http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip}
-WARNING: This is large ($~$300MB) and will take some time to download.
+WARNING: This is large (about 300MB) and will take some time to download.
}
-\exstep{Unpack the archiveÕs contents to a place on your machine with at least
+\exstep{Unpack the archive's contents to a place on your machine with at least
2GB of free space.
-(On windows, right click on the archive, and use the ÔExtract archive..Õ option).
+(On Windows, right click on the archive, and use the 'Extract archive..' option).
}
\exstep{Open the newly extracted directory and double click the VMWare virtual
machine configuration file (jabaws.vcf). This will launch the VMWare player.
}
-\exstep{Once VMWare player has started up, it may ask the question Ôdid you move or copy
-this virtual appliance?Õ Ð select ÔcopyÕ.}
-\exstep{You may be prompted to download the VMWare linux tools Ð these are not
-necessary, so close the window or click on ÔlaterÕ}
+\exstep{Once VMWare player has started up, it may ask the question ``Did you move or copy
+this virtual appliance?'' -- select `Copy'.}
+\exstep{You may be prompted to download the VMWare linux tools. These are not
+necessary, so close the window or click on `Later'.}
\exstep{You may also be prompted to install support for one or more devices (USB
-or otherwise) Ð say no to these options.}
+or otherwise). Say `No' to these options.}
\exstep{Once the machine has loaded, it will display a series of IP addresses
-for the different services provided by the VM. Make a note of the JABAWS URL Ð
-this will begin with Ôhttp:Õ and end with Ô/jabawsÕ.}
+for the different services provided by the VM. Make a note of the JABAWS URL --
+this will begin with `http:' and end with `/jabaws''.}
}
\exercise{Configuring Jalview to access your new JABAWS virtual appliance}{
menu.
{\sl Alternately, use the System Java console if you have
-configured it to open when Jalview is launched, via your systemÕs Java
-preferences (under the ÔAdvancedÕ tab on Windows).}}
-\exstep{Open the preferences dialog and locate the Web Services preferences.}
+configured it to open when Jalview is launched, {\sl via} your system's Java
+preferences (under the `Advanced' tab on Windows).}}
+\exstep{Open the {\sl Preferences} dialog and locate the Web Services tab.}
\exstep{Add the URL for the new JABAWS server you started in Exercise
-\ref{jabawsvmex} to the list of JABAWS urls using the ÔNew Service
-URLÕ button.}
-\exstep{You will be asked if you want to test the service. Hit ÔYesÕ to do this
-Ð- you should then see some output in the console window.
+\ref{jabawsvmex} to the list of JABAWS urls using the `New Service
+URL' button.}
+\exstep{You will be asked if you want to test the service. Hit `Yes' to do this
+-- you should then see some output in the console window.
{\sl Take a close look at the output in the console. What do you think is
happening?}
}
-\exstep{Hit {\sl OK} to save your preferences Ð- you have now added a new JABA
+\exstep{Hit OK to save your preferences -- you have now added a new JABA
service to Jalview!}
\exstep{Try out your new JABA services by loading the ferredoxin sequences from
http://www.jalview.org/tutorial/alignment.fa}
\exstep{Launch an alignment using one
-of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the web services menu on the alignment window.
+of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the {\sl Web Service} menu on the alignment window.
{\sl Note: You can watch the JABA VM appliance's process working by opening the
process monitor on your system. (On Windows XP, this involves right-clicking the
-system clock and opening the task manager Ð- then selecting the ÔProcessesÕ tab
+system clock and opening the task manager -- then selecting the 'Processes' tab
and sort by CPU).}
}
}
\subsubsection{Resetting the JABA services setting to their defaults}
-Once you have configured a JABAWS server and selected the `OK' button of the
+Once you have configured a JABAWS server and selected the OK button of the
preferences menu, the settings will be stored in your Jalview preferences file,
along with any preferences regarding the layout of the web services menu. If
you should ever need to reset the JABAWS server list to its defaults, use the
\section{Multiple Sequence Alignment}
\label{msaservices}
Sequences can be aligned using a range of algorithms provided by JABA web
-services. These include ClustalW,\footnote{{\sl ``CLUSTAL W: improving the
+services. These include ClustalW\footnote{{\sl ``CLUSTAL W: improving the
sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."} Thompson JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic
-Acids Research} {\bf 22}, 4673-80} Muscle,\footnote{{\sl ``MUSCLE: a multiple
+Acids Research} {\bf 22}, 4673-80}, Muscle\footnote{{\sl ``MUSCLE: a multiple
sequence alignment method with reduced time and space complexity"} Edgar, R.C.
-(2004) {\sl BMC Bioinformatics} {\bf 5}, 113} MAFFT,\footnote{{\sl ``MAFFT: a
+(2004) {\sl BMC Bioinformatics} {\bf 5}, 113}, MAFFT\footnote{{\sl ``MAFFT: a
novel method for rapid multiple sequence alignment based on fast Fourier
transform"} Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) {\sl
Nucleic Acids Research} {\bf 30}, 3059-3066. and {\sl ``MAFFT version 5:
improvement in accuracy of multiple sequence alignment"} Katoh, K., Kuma, K.,
-Toh, H. and Miyata, T. (2005) {\sl Nucleic Acids Research} {\bf 33}, 511-518.}
+Toh, H. and Miyata, T. (2005) {\sl Nucleic Acids Research} {\bf 33}, 511-518.},
ProbCons\footnote{PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
-(2005) {\sl Genome Research} {\bf 15} 330-340.} and T-COFFEE.\footnote{T-Coffee:
-A novel method for multiple sequence alignments. (2000) Notredame,Higgins and Heringa {\sl JMB} {\bf 302} 205-217} Of these,
-T-COFFEE is the slowest, but also the most accurate. ClustalW is historically the most widely used. Muscle is faster than ClustalW and probably the most accurate for smaller alignments and MAFFT is probably the best for large
+(2005) {\sl Genome Research} {\bf 15} 330-340.} and T-COFFEE\footnote{T-Coffee:
+A novel method for multiple sequence alignments. (2000) Notredame, Higgins and
+Heringa {\sl JMB} {\bf 302} 205-217}. Of these, T-COFFEE is the slowest, but also the most accurate. ClustalW is historically the most widely used. Muscle is faster than ClustalW and probably the most accurate for smaller alignments and MAFFT is probably the best for large
alignments\footnote{Clustal Omega, which was released in 2011, is arguably the
fastest and most accurate tool for protein multiple alignment, and is
included in JABAWS 2.0.}.
results, in this case an alignment. By default, the new alignment will be
ordered in the same way as the input sequences; however, many alignment programs
re-order the input to place homologous sequences close together. This ordering
-can be recovered using the `Original ordering' entry within the {\sl Calculation
+can be recovered using the `Original ordering' entry within the {\sl Calculate
$\Rightarrow$ Sort } sub menu.
\begin{figure}[htbp]
\subsubsection{Alignments of sequences that include hidden regions}
-If the view or selected region that is submitted for alignment contains hidden regions, then only the visible sequences will be submitted to the service. Furthermore, each contiguous segment of sequences will be aligned independently (resulting a number of alignment `subjobs' appearing in the status window). Finally, the results of each subjob will be concatenated with the hidden regions in the input data prior to their display in a new window. This approach ensures that 1) hidden column boundaries in the input data are preserved in the resulting alignment - in a similar fashion to the constraint that hidden columns place on alignment editing (see Section \ref{lockededits}). 2) hidden columns can be used to preserve existing parts of an alignment whilst the visible parts are locally refined.
+If the view or selected region that is submitted for alignment contains hidden regions, then {\bf only the visible sequences will be submitted to the service}. Furthermore, each contiguous segment of sequences will be aligned independently (resulting in a number of alignment `subjobs' appearing in the status window). Finally, the results of each subjob will be concatenated with the hidden regions in the input data prior to their display in a new window. This approach ensures that 1) hidden column boundaries in the input data are preserved in the resulting alignment - in a similar fashion to the constraint that hidden columns place on alignment editing (see Section \ref{lockededits}), and 2) hidden columns can be used to preserve existing parts of an alignment whilst the visible parts are locally refined.
\exercise{Multiple Sequence Alignment}{
\exstep{ Close all windows and open the alignment at {\sf
http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
-Web Service $\Rightarrow$ Alignment $\Rightarrow$ Default Settings} for Muscle. A window will open giving the job status. After a short time, a second window will open with the results of the alignment.} \exstep{Select the first sequence set by clicking on the window and try running ClustalW and MAFFT (from the {\sl Web Services $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and you should notice small differences. }
+Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}. A window will open giving the job status. After a short time, a second window will open with the results of the alignment.} \exstep{Select the first sequence set by clicking on the window and try running ClustalW and MAFFT (from the {\sl Web Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and you should notice small differences. }
\exstep{Select the last three sequences in the MAFFT alignment, and de-align them with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect them and then submit the view for re-alignment with ClustalW.}
\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment. Once the ClustalW re-alignment has completed, compare the results of re-alignment of the three sequences with their alignment in the original MAFFT result.}
-\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them. Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ MAFFT} to submit the visible portion of the alignment to MAFFT. When the web service job pane appears, note that there are now two alignment job status panes shown in the window.}
+\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them. Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to submit the visible portion of the alignment to MAFFT. When the web service job pane appears, note that there are now two alignment job status panes shown in the window.}
\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible region in the result with the corresponding region of the original alignment. If you wish, select and hide a few more columns in the N-terminal region, and submit the alignment to the service again and explore the effect of local alignment on the non-homologous parts of the N-terminal region.}
}
\subsubsection{Getting help on the parameters for a service}
Each parameter available for a method usually has a short description, which
jalview will display as a tooltip, or as a text pane that can be opened under
-the parameterÕs controls. In the parameter shown in Figure
+the parameter's controls. In the parameter shown in Figure
\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
service can also be accessed, by right clicking the button and selecting a URL
from the pop-up menu that will open.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2.5in]{images/clustalwparamdetail.pdf}
-\caption{{\bf ClustalW parameter slider detail}. From the ClustalW {\sl Edit &
-Run ..} dialog box. }
+\caption{{\bf ClustalW parameter slider detail}. From the ClustalW {\sl Clustal $\Rightarrow$ Edit settings and run ...} dialog box. }
\label{clustalwparamdetail}
\end{center}
\end{figure}
The different multiple alignment algorithms available from JABA vary greatly in
the number of adjustable parameters, and it is often difficult to identify what
are the best values for the sequences that you are trying to align. For these
-reasons, each JABA service may provide one or more presets Ð which are
+reasons, each JABA service may provide one or more presets -- which are
pre-defined sets of parameters suited for particular types of alignment
problem. For instance, the Muscle service provides the following presets:
\begin{list}{$\bullet$}{}
\item Nucleotide alignments (fastest speed)
\end{list}
-The presets are displayed in the JABA web services submenu, and can also
+The presets are displayed in the JABA web services submenu, and can also be
accessed from the parameter editing dialog box, which is opened by selecting
-the Ô{\sl Edit and run..}Õ option from the web serviceÕs menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web service�s menu. If you have used
a preset, then it will be mentioned at the beginning of the job status file shown
in the web service job progress window.
\subsubsection{Alignment Service Limits}
Multiple alignment is a computationally intensive calculation. Some JABA server
services and service presets only allow a certain number of sequences to be
-aligned Ð the precise number will depend on the server that you are using to
+aligned. The precise number will depend on the server that you are using to
perform the alignment. Should you try to submit more sequences than a service
can handle, then an error message will be shown informing you of the maximum
number allowed by the server.
\subsection{User defined Presets}
Jalview allows you to create your own presets for a particular service. To do
-this, select the `{\sl Edit parameters and run ..}' option for your service,
+this, select the `{\sl Edit settings and run ...}' option for your service,
which will open a parameter editing dialog box like the one shown in Figure
\ref{jwsparamsdialog}.
The top row of this dialog allows you to browse the existing presets, and
when editing a parameter set, allows you to change its nickname. As you
adjust settings, buttons will appear at the top of the parameters dialog that
-allow you to create, update, delete or undo changes to the currently selected
-user preset. In addition to the parameter set name, you can also provide a short
+allow you to Revert or Update the currently selected user preset with your changes, Delete the current preset, or Create a new preset, if none exists with the given name. In addition to the parameter set name, you can also provide a short
description for the parameter set, which will be shown in the tooltip for the
parameter set's entry in the web services menu.
\begin{list}{$\circ$}{}
\item If nothing is selected, Jalview will check the length of each alignment row to determine if the visible sequences in the view are aligned.
\begin{list}{-}{}
- \item If all rows are the same length (often due to the application of the {\sl Edit $\Rightarrow$ Pad Gaps} option), then a JNet prediction will be run for the first sequence in the alignment, using the current alignment as the profile to use for prediction.
- \item Otherwise, just the first sequence will be submitted for a full JNet prediction.
+ \item If all rows are the same length (often due to the
+ application of the {\sl Edit $\Rightarrow$ Pad Gaps} option), then
+ a JPred prediction will be run for the first sequence in the
+ alignment, using the current alignment as the profile to use for prediction.
+ \item Otherwise, just the first sequence will be submitted for a
+ full JPred prediction.
\end{list}
-\item If just one sequence (or a region on one sequence) has been selected, it will be submitted to the automatic JNet prediction server for homolog detection and prediction.
-\item If a set of sequences are selected, and they appear to be aligned using the same criteria as above, then the alignment will be used for a Jnet prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
+\item If just one sequence (or a region in one sequence) has been selected, it
+will be submitted to the automatic JPred prediction server for homolog detection
+and prediction.
+\item If a set of sequences are selected, and they appear to be aligned using
+the same criteria as above, then the alignment will be used for a JPred
+prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
\end{list}
Jpred is launched in the same way as the other web services. Select {\sl Web
Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
-Secondary Structure Prediction} from the alignment window menu
-(Figure \ref{jpred}). A status window opens to inform you of the progress of
-the job. Upon completion, a new alignment window opens and the Jpred
+Secondary Structure Prediction}{\footnote JNet is the Neural Network based
+secondary structure prediction method that the JPred server uses.} from the
+alignment window menu (Figure \ref{jpred}).
+A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
predictions are included as annotations. Consult the Jpred documentation for
information on interpreting these results.
Hidden columns can be used to exclude parts of a sequence or profile from the
input sent to the JNet service. For instance, if a sequence is known to include
a large loop insertion, hiding that section prior to submitting the JNet
-prediction may result in a more reliable\footnote{This, of course, cannot be guaranteed, but the profile
-calculated by JNet will at least be different.} secondary structure prediction
-either side of the insertion. Prediction results returned from the service will
+prediction can produce different results. In some cases, these secondary structure predictions can be more reliable for sequence on either side of the insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results returned from the service will
be mapped back onto the visible parts of the sequence, to ensure a single frame
of reference is maintained in your analysis.
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
-\exstep{ Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} from the alignment window menu. A status window will appear and after some time a new window with the JPred prediction will appear. Note that the number of sequences in the results window is many more than in the original alignment as JNet performs a PSI-BLAST search to expand the prediction dataset.
+\exstep{ Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear. Note that the number of sequences in the results window is many more than in the original alignment as JNet performs a PSI-BLAST search to expand the prediction dataset.
}
% TODO: check how long this takes - about 2 mins once it gets on the cluster.
\exstep{
Select a different sequence and perform a JNet prediction in the same way. There will probably be minor differences in the predictions.
}
\exstep{
-Select the second sequence prediction, and copy and paste it into the first prediction window. You can now compare the two predictions. Jnet secondary structure prediction annotation are examples of {\bf sequence associated alignment annotation}.
+Select the second sequence prediction, and copy and paste it into the first
+prediction window. You can now compare the two predictions. Jnet secondary structure prediction annotations are examples of {\bf sequence-associated alignment annotation}.
% which is described in Section \ref{seqassocannot} below.
}
\exstep{
\label{featannot}
Features and annotations are additional information that is overlaid on the sequences and the alignment. Generally speaking, annotations are associated with columns in the alignment. Features are associated with specific residues in the sequence.
-Annotations are rendered below the alignment, in the annotation panel, and often reflect properties of the alignment as a whole. The conservation, consensus and quality scores are examples of dynamic annotation. As the alignment changes, these annotations will change along with it. Conversely, sequence features are properties of the individual sequences. They do not change with the alignment, but are shown mapped on to specific residues within the alignment.
+Annotations are shown below the alignment in the annotation panel, and often reflect properties of the alignment as a whole. The Conservation, Consensus and Quality scores are examples of dynamic annotation, so as the alignment changes, they change along with it. Conversely, sequence features are properties of the individual sequences, so they do not change with the alignment, but are shown mapped on to specific residues within the alignment.
-Features and annotation can be interactively created, or retrieved from external data sources. DAS (the Distributed Annotation System) is the primary source of sequence features, whilst webservices like JPred (see \ref{jpred} above) can be used to analyse a given sequence or alignment and generate annotation for it.
+Features and annotation can be interactively created, or retrieved from external
+data sources. DAS (the Distributed Annotation System) is the primary source of
+sequence features, whilst webservices like JNet (see \ref{jpred} above) can be used to analyse a given sequence or alignment and generate annotation for it.
\subsection{Creating sequence features}
$\Rightarrow$ Show Sequence Features} menu option. When multiple features are
present it is usually necessary to customise the display. Jalview allows the
display, colour, rendering order and transparency of features to be modified
-via the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
+{\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
brings up a dialogue window (Figure \ref{custfeat}) which allows the
visibility of individual feature types to be selected, colours changed (by
clicking on the colour of each sequence feature type) and the rendering order
\exstep{
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
appropriate box. Click on the Feature Colour bar to change the colour if
-desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at position 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
+desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at column 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
}
\exstep{
Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
this so that you can see the features you have just created. Click the check
box for ``Iron binding site" under {\sl Display} and note that display of this
feature type is now turned off. Click it again and note that the features are
-now displayed. Close the sequence feature settings box by clicking {\sl OK} or
-{\sl Cancel}.} }
+now displayed. Close the sequence feature settings box by clicking OK or
+Cancel.} }
\subsection{Creating user defined annotation}
\end{figure}
\exercise{Annotating alignments}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} to bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}. Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
+\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} to bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}. Enter ``Iron binding site" and click OK. A new, empty, row appears.
}
\exstep{
-Navigate to column 97. Select column 97 on the new annotation row. Right click on the selection and select {\sl Label} from the context menu. Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again and select {\sl Colour}. Choose a colour from the colour chooser dialogue and click {\sl OK}. Press [ESC] to remove the selection.
+Navigate to column 97. Select column 97 on the new annotation row. Right click on the selection and select {\sl Label} from the context menu. Enter ``Fe" in the box and click OK. Right-click on the selection again and select {\sl Colour}. Choose a colour from the colour chooser dialogue and click OK. Press [ESC] to remove the selection.
}
\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet arrow.
}
\exstep{Export the file to a text editor and edit the file to change the name of the annotation row. Save the file and drag it onto the alignment view.}
\exstep{Try to add an additional helix somewhere along the row by editing the file and re-importing it.
{\sl Hint: Use the {\bf Export Annotation} function to view what helix annotation looks like in a jalview annotation file.}}
-\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotation..} function to export all the alignment's annotation to a file.}
+\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...} function to export all the alignment's annotation to a file.}
\exstep{Open the exported annotation in a text editor, and use the {\bf Annotation File Format} documentation to modify the style of the Conservation, Consensus and Quality annotation rows so they appear as several lines on a single line graph.
{\sl Hint: You need to change the style of annotation row in the first field of the annotation row entry in the file, and create an annotation row grouping to overlay the three quantitative annotation rows.}
}
\label{viewannotfileex}\exstep{Recover or recreate the secondary structure
-prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the jnet secondary structure prediction annotation row. Note the {\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the annotation. } }
+prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row. Note the {\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the annotation. } }
\section{Importing features from databases}
\label{featuresfromdb}
Jalview includes a function to automatically verify and update each sequence's
start and end numbering against any of the sequence databases that the {\sl
Sequence Fetcher} has access to. This function is accessed from the {\sl
-Webservices $\Rightarrow$ Fetch DB References} sub-menu in the Alignment
+Webservice $\Rightarrow$ Fetch DB References} sub-menu in the Alignment
window. This menu allows you to query either the set of {\sl Standard
Databases}, which includes EMBL, Uniprot, the PDB, and the currently selected
DAS sequence sources, or just a specific datasource from one of the submenus.
\exstep{Verify that there are no database references for the sequences by first
checking that the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show
Database IDs} option is selected, and then mousing over each sequence's ID.}
-\exstep{Use the {\sl Webservices $\Rightarrow$ Fetch DB References} menu option to retrieve database IDs for the sequences.}
+\exstep{Use the {\sl Webservice $\Rightarrow$ Fetch DB References} menu option to retrieve database IDs for the sequences.}
\exstep{Examine the tooltips for each sequence in the alignment as the retrieval progresses - note the appearance of new database references.}
\exstep{Once the process has finished, save the alignment as a Jalview Project.
\subsection{Retrieving Features {\sl via} DAS}
\label{dasfretrieval}
Jalview includes a client to retrieve features from DAS annotation servers. To
-retrieve features, select {\sl View $\Rightarrow$ Feature Settings\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab in the Feature Settings Window (Figure \ref{das}). A list of DAS sources compiled from the currently configured DAS registry\footnote{By default, this will be the major public DAS server registry maintained by the Sanger Institute: http://www.dasregistry.org} is shown in the left hand pane. Highlighting an entry on the left brings up information about that source in the right hand panel.
+retrieve features, select {\sl View $\Rightarrow$ Feature Settings\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab in the Sequence Feature Settings Window (Figure \ref{das}). A list of DAS sources compiled from the currently configured DAS registry\footnote{By default, this will be the major public DAS server registry maintained by the Sanger Institute: http://www.dasregistry.org} is shown in the left hand pane. Highlighting an entry on the left brings up information about that source in the right hand panel.
\begin{figure}[htbp]
\begin{center}
\subsubsection{The Fetch Uniprot IDs dialog box}
\label{discoveruniprotids}
-If any sources are selected which refer to Uniprot coordinates as their reference system, then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing [OK] instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Services $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}. If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record to ensure that features retrieved from the DAS source are rendered at the correct position.
+If any sources are selected which refer to Uniprot coordinates as their reference system, then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing OK instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Service $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}. If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record to ensure that features retrieved from the DAS source are rendered at the correct position.
\subsubsection{Rate of feature retrieval}
Feature retrieval can take some time if a large number of sources is selected and if the alignment contains a large number of sequences. This is because Jalview only queries a particular DAS source with one sequence at a time, to avoid overloading it. As features are retrieved, they are immediately added to the current alignment view. The retrieved features are shown on the sequence and can be customised as described previously.
\exercise{Retrieving features with DAS}{
\label{dasfeatretrexcercise}
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View $\Rightarrow$ Sequence Features\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment.
-}
-\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
+$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
+the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click OK. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment. } \exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Sequence Feature Settings window. }
\exstep{Move the mouse over the sequence ID panel. Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
\exstep{Search through the alignment to find a feature with a link symbol next to it. Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
\exstep{
-Select {\sl View $\Rightarrow$ Feature Settings\ldots} to reopen the Feature Settings window. All the loaded feature types should now be displayed. Those at the top of the list sit on top of and obscure those below. Move the feature settings window so that the alignment is visible and uncheck some of the feature types by clicking the tick box in the display column. Observe how the alignment display changes. Note that unselected feature types do not appear in the tool tip.
+Select {\sl View $\Rightarrow$ Feature Settings\ldots} to reopen the Feature Settings window. All the loaded feature types should now be displayed. Those at the top of the list are drawn on top of those below, obscuring them in the alignment view where they overlap. Move the feature settings window so that the alignment is visible and uncheck some of the feature types by clicking the tick box in the display column. Observe how the alignment display changes. Note that unselected feature types do not appear in the tool tip.
}
\exstep{Reorder the features by dragging feature types up and down the order in the Feature Settings panel. e.g. Click on {\sl CHAIN} then move the mouse downwards to drag it below {\sl DOMAIN}. Note that {\sl DOMAIN} is now shown on top of {\sl CHAIN} in the alignment window. Drag {\sl METAL} to the top of the list. Observe how the cysteine residues are now highlighted as they have a {\sl METAL} feature associated with them.
}
\exstep{Press the {\sl Optimise Order} button. The features will be ordered according to increasing length, placing features that annotate shorter regions of sequence higher on the display stack.}
-\exstep{Select {\sl File $\Rightarrow$ Export Features} from the Alignment window. You can choose to export the retrieved features as a GFF file, or Jalview's own Features format.
+\exstep{Select {\sl File $\Rightarrow$ Export Features\ldots} from the Alignment window. You can choose to export the retrieved features as a GFF file, or Jalview's own Features format.
% TODO: describe working with features files and GFF
}
}
of a particular type are the result of a specific type of database query or calculation. Here, they may also carry information within their textual description, or most commonly for calculations, a score related to the property being investigated. Jalview can shade sequence
features using a graduated colourscheme in order to highlight these variations.
In order to apply a graduated scheme to a feature type, select the `Graduated
-colour' entry in the Sequence feature type's popup menu, which is opened by
-right-clicking the feature type's color in the settings dialog box. Two types
+colour' entry in the Sequence {\sl Feature Type}'s popup menu, which is opened by
+right-clicking the {\sl Feature Type} or {\sl Color} in the {\sl Sequence Feature Settings} dialog box. Two types
of colouring styles are currently supported: the default is quantitative
colouring, which shades each feature based on its score, with the highest
scores receiving the `Max' colour, and the lowest scoring features coloured
Uniprot's `DOMAIN' feature - where the actual type of domain is given in the
feature's description.
-Graduated feature colour schemes can also be used to exclude low or
+Graduated feature colourschemes can also be used to exclude low or
high-scoring features from the alignment display. This is done by choosing your
desired threshold type (either above or below), using the drop-down menu in the
dialog box. Then, adjust the slider or enter a value in the text box to set the
The feature settings dialog box allows you to toggle between a graduated and
simple feature colourscheme using the pop-up menu for the feature type. When a
-graduated scheme is applied, it will be indicated by in the colour column for
+graduated scheme is applied, it will be indicated in the colour column for
that feature type - with coloured blocks or text to indicate the colouring
style and a greater than ($>$) or less than ($<$) symbol to indicate when a
threshold has been defined.
sequence features present on each sequence, and also according to any scores
associated with a feature. Each of these buttons uses the currently displayed
features to determine the ordering, but
-if you wish to re-order the alignment using a single type of feature, then you can do this from the feature type's
-popup menu. Simply right-click the type's style in the Feature Settings dialog
-box, and select one of the {\sl Sort by score} and {\sl Sort by density}
+if you wish to re-order the alignment using a single type of feature, then you can do this from the {\sl Feature Type}'s
+popup menu. Simply right-click the type's style in the Sequence Feature Settings dialog
+box, and select one of the {\sl Sort by Score} and {\sl Sort by Density}
options to re-order the alignment. Finally, if a specific region is selected,
then only features found in that region of the alignment will be used to
create the new alignment ordering.
displayed. Mouse over the annotation and also export and examine the GFF and
Jalview features file to better understand how the hydrophobicity measurements
are recorded.}
-\exstep{Apply a graduated colourscheme to the hydrophobicity annotation to
+\exstep{Apply a {\sl Graduated Colour} to the hydrophobicity annotation to
reveal the variation in average hydrophobicity across the alignment.}
\exstep{Select a range of alignment columns, and use one of the sort by feature buttons to order the alignment according to that region's average
hydrophobicity.}
\label{threshgradfeaturesex}
\exstep{Reusing the annotated alignment from exercise
\ref{shadingorderingfeatsex}, experiment with the colourscheme threshold to
-highlight the most, or least hydrophobic regions. Note how the colour scheme icon for the feature type changes when you change the threshold type.}
+highlight the most, or least hydrophobic regions. Note how the {\sl Colour} icon for the {\sl Feature Type} changes when you change the threshold type and press OK.}
\exstep{Change the colourscheme so
that features at the threshold are always coloured grey, and the most
hydrophobic residues are coloured red, regardless of the threshold value
\exstep{Enable the Uniprot {\em chain} annotation in the feature settings
display and re-order the features so it is visible under the hydrophobicity
annotation.}
-\exstep{Apply a graduated colourscheme to the {\em chain}
+\exstep{Apply a {\sl Graduated Colour} to the {\em chain}
annotation so that it distinguishes the different canonical names associated
with the mature polypeptide chains.}
-\exstep{Export the alignment's sequence features using the Jalview sequence
-feature file format, to see how the different types of graduated feature
+\exstep{Export the alignment's sequence features using the Jalview and GFF file formats, to see how the different types of graduated feature
colour styles are encoded. }
}
\section{Working with DNA}
\label{workingwithnuc}
Jalview was originally developed for the analysis of protein sequences, but
now includes some specific features for working with nucleic acid sequences
-and alignments. Nucleotide sequences and alignments are recognised based on
+and alignments. Jalview recognises nucleotide sequences and alignments based on
the presence of nucleotide symbols [ACGT] in greater than 85\% of the
sequences. Built in codon-translation tables can be used to translate ORFs
-into peptides for further analysis. EMBL records retrieved {\sl via} the
+into peptides for further analysis. EMBL nucleotide records retrieved {\sl via} the
sequence fetcher (see Section \ref{fetchseq}) are also parsed in order to
identify codon regions and extract peptide products. Furthermore, Jalview
records mappings between protein sequences that are derived from regions of a
Jalview provides a simple colourscheme for DNA bases, but does not apply any
specific conservation or substitution score model for the shading of
-nucleotide alignments. However, pairwise alignments performed using the {\sl
-Alignment Window $\Rightarrow$ Calculations $\Rightarrow$ Pairwise Alignment
+nucleotide alignments. However, pairwise alignments performed using the {\sl Calculate $\Rightarrow$ Pairwise Alignment
\ldots} option will utilise an identity score matrix to calculate alignment
score when aligning two nucleotide sequences.
\subsubsection{Aligning Nucleic Acid Sequences}
-Jalview only has limited knowledge of the capabilities of the programs that
+Jalview has limited knowledge of the capabilities of the programs that
are made available to it {\sl via} web services, so it is up to you, the user,
to decide which service to use when working with nucleic acid sequences. The
-table below shows which alignment programs are appropriate for nucleotide alignment.
+table below shows which alignment programs are most appropriate
+for nucleotide alignment. Generally, all will work, but some may be more suited
+to your purposes than others. We also note that none of these include
+support for taking RNA secondary structure prediction into account when aligning
+sequences. We expect that in the future, Jalview will fully support secondary
+structure aware RNA alignment.
\begin{table}{}
\centering
\begin{tabular}{|l|c|l|}
+\hline
Program& NA support& Notes\\
\hline
ClustalW& Yes&\begin{minipage}[f]{3in}
sequences. Editable parameters include nucleotide substitution matrices and
distance metrics.
\end{minipage}
+
\\
\hline
+
Muscle& Yes (treat U as T)&\begin{minipage}[f]{3in}
Default is to autodetect nucleotide
sequences. Editable parameters include nucleotide substitution matrices and
distance metrics.
\end{minipage}
+
\\
\hline
+
MAFFT& Yes&\begin{minipage}[f]{3in}
Will autodetect nucleotide sequences and use a hardwired substitution model
(all amino-acid sequence related parameters are ignored). Unknown whether
substitution model treats Uracil specially.
\end{minipage}
+
\\
\hline
+
ProbCons& No&\begin{minipage}[f]{3in}
ProbCons has no special support for aligning nucleotide sequences. Whilst an
alignment will be returned, it is unlikely to be reliable.
\end{minipage}
+
\\
\hline
+
T-COFFEE& Yes&\begin{minipage}[f]{3in}
Sequence type is automatically detected and an appropriate
parameter set used as required. A range of nucleotide specific
score models are available.\end{minipage}
-\\
+
+\\\hline
\end{tabular}
\caption{{\bf JABAWS Alignment programs suitable for aligning nucleic acid
sequences.} All JABAWS alignment services will return an alignment if provided
-with RNA or DNA sequences, with varying reliability. No programs include
-support for taking RNA secondary structure prediction into account when
-aligning sequences.}
+with RNA or DNA sequences, with varying reliability.}
\label{nucleomsatools}
\end{table}
\subsection{Translate cDNA}
-The {\sl Calculations $\Rightarrow$ Translate cDNA} function in the alignment
-window is only available when working with a nucleic acid alignment. It uses the standard codon translation table given in the online help to translate a nucleotide alignment, or the currently selected region, into a set of aligned peptide sequences. Any features or annotation present on the nucleotide alignment will also be translated, allowing DNA alignment analysis results to be transferred on to peptide products for further investigation.
+The {\sl Calculate $\Rightarrow$ Translate cDNA} function in the alignment
+window is only available when working with a nucleic acid alignment. It uses the standard codon translation table given in the online help documentation to translate a nucleotide alignment, or the currently selected region, into a set of aligned peptide sequences. Any features or annotation present on the nucleotide alignment will also be translated, allowing DNA alignment analysis results to be transferred on to peptide products for further investigation.
\subsection{Linked DNA and Protein Views}
\parbox{3.5in}{
-Views of alignments involving DNA sequences are linked to views of alignments containing their peptide products in a similar way to views of protein sequences and views of their associated structures. Peptides translated from cDNA and extracted from EMBL records for DNA contigs are linked to their `parent' coding regions. Mousing over a region of the peptide highlights codons in views showing the original coding region.
+Views of alignments involving DNA sequences are linked to views of alignments containing their peptide products in a similar way to views of protein sequences and views of their associated structures. Peptides translated from cDNA that have been fetched from EMBL records for DNA contigs are linked to their `parent' coding regions. Mousing over a region of the peptide highlights codons in views showing the original coding region.
}\parbox{3in}{
\begin{center}
%\begin{figure}[htbp]
Uniprot sequence's coordinate system with the coding regions annotated on the
EMBL sequence. Jalview utilises cross-reference information in two ways.
\subsubsection{Retrieval of Protein or DNA Cross References}
-The {\sl Calculations $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the product(s).
+The {\sl Calculate $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the protein product(s).
\subsubsection{Retrieval of protein DAS features on coding regions}
-The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments. This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig. Jalview will use the Uniprot accessions associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using the coding region location.
+The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments. This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig. Jalview will use the Uniprot accession numbers associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using the coding region location.
\begin{figure}[htbp]
\begin{center}
{
\exstep{Use the sequence fetcher to retrieve EMBL record V00488.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the alignment view format to Wrapped mode so the distinct exons can be seen.}
-\exstep{Open the DAS sequence feature fetcher window and fetch features for V00488 the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
+\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for V00488 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
\exstep{Mouse over the features retrieved, note that they have been mapped onto the coding regions, and in some cases broken into several parts to cover the distinct exons.}
-\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculations $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
+\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculate $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
}
}
% \subsection{Working with Modeller files}
% \subsection{Using local PDB files}
% \section{Pairwise alignments}
-\r \end{document}
+
+ \end{document}
git://source.jalview.org / jalview-manual.git / blobdiff