{\Huge
-Jalview 2.8
+Jalview 2.8.2
}
\vspace{0.5in}
{\huge
-A manual and introductory tutorial }
+Manual and Introductory Tutorial }
\vspace{2.4in}
{\large
-David Martin, James Procter, Andrew Waterhouse, Saif Shehata and Geoff Barton
+David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,
+Suzanne Duce and Geoff Barton
-With additional material by Nancy Giang.
+
}
\vspace{1.2in}
\vspace{2in}
-Manual version 1.4.1
+Manual Version 1.5.1
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-18th January 2013
+
+24th April 2015
\end{center}
\subsection{Jalview}
Jalview is a multiple sequence alignment viewer, editor and analysis tool.
Jalview is designed to be platform independent (running on Mac, MS Windows, Linux
-and any other platform that supports Java), capable of editing and analysing
-large alignments (thousands of sequences) with minimal degradation in
+and any other platforms that support Java). Jalview is capable of editing and
+analysing large alignments (thousands of sequences) with minimal degradation in
performance, and able to show multiple integrated views of the alignment and
other data. Jalview can read and write many common sequence formats including
FASTA, Clustal, MSF(GCG) and PIR.
-There are two types of Jalview program. The {\bf Jalview Desktop} is a stand
-alone application that provides powerful editing, visualization, annotation and
+There are two types of Jalview program. The {\bf Jalview Desktop} is a standalone
+application that provides powerful editing, visualization, annotation and
analysis capabilities. The {\bf JalviewLite} applet has the same core
visualization, editing and analysis capabilities as the desktop, without the
desktop's webservice and figure generation capabilities. It is designed to be
embedded in a web page,\footnote{A demonstration version of Jalview (Jalview Micro
Edition) also runs on a mobile phone but the functionality is limited to sequence
-colouring.} and includes a javascript API to allow customisable display of alignments for web sites such as
-{\bf pfam}.\footnote{\url{http://pfam.sanger.ac.uk}}
+colouring.} and includes a javascript API to allow customisable display of
+alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
-Jalview 2.8 was released in November 2012. The Jalview Desktop in this version
+Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
provides access to protein and nucleic acid sequence, alignment and structure
databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. A
\subsection{Jalview's Capabilities}
% TODO add references to appropriate sections for each capability described here.
-Figure \ref{jvcapabilities} gives an overview of the main features of the Jalview desktop application. Its primary function is the editing and visualization of sequence alignments, and their interactive analysis. Tree building, principal components analysis, physico-chemical property conservation and sequence consensus analyses are built in to the program. Web services enable Jalview to access remote alignment and secondary structure prediction programs, as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
+Figure \ref{jvcapabilities} gives an overview of the main features of the
+Jalview desktop application. Its primary function is the editing and
+visualization of sequence alignments, and their interactive analysis. Tree
+building, principal components analysis, physico-chemical property conservation
+and sequence consensus analyses are built into the program. Web services enable
+Jalview to access online alignment and secondary structure prediction programs,
+as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5.8in]{images/jvcapabilities.pdf}
between Jalview, TOPALi and AstexViewer.} in 2004, enabling Andrew Waterhouse and
Jim Procter to re-engineer the original program to introduce contemporary developments
in bioinformatics and take advantage of the latest web and Java technology.
-Jalview's development is now supported for a further 5 years from October 2009
-by an award from the BBSRC's Tools and Resources fund. In 2010, 2011, and 2012, Jalview
-benefitted from the \href{http://code.google.com/soc/}{Google Summer of Code},
-when Lauren Lui and Jan Engelhardt introduced new features for handling RNA
-alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
+Jalview's development has been supported from 2009
+by awards from the BBSRC's Tools and Resources fund, and, since 2014, a Wellcome Trust Biomedical Resource grant\footnote{Wellcome grant number 101651/Z/13/Z}. In 2010, 2011, and 2012, Jalview benefitted from the
+\href{http://code.google.com/soc/}{Google Summer of Code}, when Lauren Lui and Jan Engelhardt introduced new features for handling RNA alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
%TODO describe future plans in history ? not a good idea.
\subsubsection{Citing Jalview}
If you use Jalview in your work you should cite:\newline
-{\sl ``Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"}\newline
-Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) \newline {\sl Bioinformatics} doi: 10.1093/bioinformatics/btp033
+{\sl "Jalview Version 2 - a multiple sequence alignment editor and analysis
+workbench"}\newline Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) \newline {\sl Bioinformatics} doi: 10.1093/bioinformatics/btp033
-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.
+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.
-\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
-basic operation of Jalview and should be sufficient for those who just want to
+basic operation of Jalview and should be sufficient for those who want to
load Jalview (Section \ref{startingjv}), open an alignment (Section \ref{loadingseqs}), perform basic editing and colouring (Section \ref{selectingandediting} and Section \ref{colours}), and produce publication
and presentation quality graphical output (Section \ref{layoutandoutput}).
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
+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.
-\section{Obtaining and starting The Jalview Desktop Application}
+\section{Obtaining and Starting the Jalview Desktop Application}
\label{startingjv}
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/download.pdf}
-\caption{{\bf Download page on the Jalview web site}}
+\caption{\bf Download page on the Jalview web site at www.jalview.org.}
\label{download}
\end{center}
\end{figure}
-This tutorial is based on the application version of Jalview, the Jalview
-Desktop. Much of the information will also be useful for users of the JalviewLite
-applet, which has the same core editing, analysis and visualization capabilities (see the
+This tutorial is based on the Jalview
+Desktop application. Much of the information will also be useful for users of
+the JalviewLite applet, which has the same core editing, analysis and visualization capabilities (see the
\href{http://www.jalview.org/examples/applets.html}{JalviewLite Applet Examples}
page for examples). The Jalview Desktop, however, is much more powerful, and
includes additional support for interaction with external web services, and
The Jalview Desktop can be run in two ways; as an application launched from the
web {\sl via} Java webstart, or as an application loaded onto your hard drive.
-The webstart version is launched from the {\bf Launch Jalview Desktop} link at
-the top-right of pages at \url{http://www.jalview.org}. To download the locally
-installable version, follow the links from the
-\href{http://www.jalview.org/download}{Download page} (Figure \ref{download}).
-These links will always launch the latest stable release of Jalview.\par
+The webstart version is launched from the pink `Launch Jalview Desktop
+button' at the top right hand side of pages of the website
+\href{http://www.jalview.org}{(www.jalview.org)}.
+To download the locally installable version, follow the links on the download
+page
+\href{http://www.jalview.org/download}{(www.jalview.org/download) }
+ (Figure \ref{download}).
+These links will launch the latest stable release of Jalview.\par
+
+%% this paragraph needs to be rewritten for the new signed certificate from Certum.
When the application is launched with webstart, two dialogs may appear before
the application starts. If your browser is not set up to handle webstart, then
click trust or accept as appropriate. The splash screen (Figure \ref{splash})
gives information about the version and build date that you are running,
information about later versions (if available), and the paper to cite in your
-publications. This information is also available on the Jalview web site and
-from the Desktop's {\sl Help $\Rightarrow$ About} menu option.
+publications. This information is also available on the Jalview web site at
+\url{http://www.jalview.org}.
%[fig 2]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/splash.pdf}
-\caption{{\bf Jalview splash screen}}
+\caption{{\bf Jalview splash screen.}}
\label{splash}
\end{center}
\end{figure}
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
+Jalview site. This behaviour can be switched off in the Jalview Desktop
+preferences dialog by unchecking the open file option.
+This alignment will look like the one in Figure \ref{startpage} (taken
from Jalview version 2.7).
%[figure 3 ]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4in]{images/start.pdf}
-\caption{{\bf Default startup for Jalview}}
+\caption{{\bf Default startup for Jalview.}}
\label{startpage}
\end{center}
\end{figure}
\subsubsection{Jalview News RSS Feed}
-From time to time, important announcements are made available to users of the
-Jalview Desktop {\sl via} the Jalview News reader. This window will open
+Announcements are made available to users of the
+Jalview Desktop {\sl via} the Jalview Newsreader. This window will open
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]
\begin{center}
\includegraphics[height=3in]{images/jvrssnews.pdf}
-\caption{{\bf The Jalview News Reader.} The news reader opens automatically
+\caption{{\bf The Jalview News Reader.} The newsreader opens automatically
when new articles are available from the Jalview Desktop's news channel.}
\label{jalviewrssnews}
\end{center}
\end{figure}
-\exercise{Starting Jalview}{
+\exercise{Launching Jalview from the Jalview Website}{
\label{start}
-\exstep{Point your web browser at the \href{http://www.jalview.org}{Jalview web site} and start Jalview by clicking on the `Launch Jalview Desktop' button.}
-\exstep{Open the Jalview Desktop's user preferences dialog (from the Tools
-menu), and untick the checkbox adjacent to the `Open file' entry in the
-`Visual' preferences tab.}
-\exstep{Click OK to save the preferences, then \em{launch {\bf another} Jalview
-instance from the web site}. The example alignment should not be
-loaded when the new Jalview instance starts up.}
-{\sl Note: Should you want to reload the example alignment, then select the
-{\em File$\Rightarrow$ From URL} entry from the Desktop menu, and click on the
-URL history button on the right hand side of the dialog box that opens.
-You can then select the example file's URL, followed by OK to open the file. } }
+\exstep{Open the Jalview web
+site \href{http://www.jalview.org}{(www.jalview.org)}
+in your web browser. Launch Jalview by clicking on the
+pink `Launch Jalview' Desktop button in the top right hand corner. This
+will download and open a jalview.jnlp webstart file.}
+\exstep {Dialogue boxes
+will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
+Internet, click Open. (Note you maybe asked to update Java, if you agree then it
+will automatically update the Java software). As Jalview opens, four demo
+Jalview windows automatically load.}
+\exstep {If
+you are having trouble, it may help changing the browser you are using, as the browsers and
+it's version may affect this process.}
+\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
+to the {\sl Tools $\Rightarrow$
+Preferences...} menu on the desktop. A `Preference'
+dialogue box opens, untick the box adjacent to the `Open file' entry in the
+`Visual' preferences tab.
+Click OK to save the preferences.}
+\exstep{Launch another Jalview workbench from the web site by clicking on the
+pink Launch button.
+The example alignment should not be loaded as Jalview starts up.}
+\exstep{To reload the original demo file select the
+{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
+the URL history button on the right hand side of the dialog box to view the
+files, select exampleFile\_2\_7.jar, then click OK.}
+{\bf Note:} Should you want to reload the example alignment or load your own
+sequence during the launch process, then go
+to the {\sl Tools $\Rightarrow$
+Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
+preferences tab, type in the URL of the sequence you want to load. This
+file will load during the start up process.\\
+
+As the jalview.jnlp file launches Jalview on your desktop, you
+may want to move this from the downloads folder to another folder.
+Opening from this file will allow Jalview to be launched offline.
+
+{\bf Help launching Jalview is available in a video on
+\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
+the website.}}
\subsection{Getting Help}
\label{gettinghelp}
-\subsubsection{Built in documentation}
+\subsubsection{Built in Documentation}
Jalview has comprehensive on-line help documentation. Select {\sl Help
$\Rightarrow$ Documentation} from the main window menu and a new window will
open (Figure \ref{help}). The appropriate topic can then be selected from the
\begin{center}
\parbox[c]{2in}{\centerline{\includegraphics[width=2.75in]{images/help1.pdf}}}
\parbox[c]{4in}{\includegraphics[width=4in]{images/help2.pdf}}
-\caption{{\bf Accessing the built in Jalview documentation}}
+\caption{{\bf Accessing the built in Jalview documentation.}}
\label{help}
\end{center}
\end{figure}
-\subsubsection{Email lists}
+\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
\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.
- Jalview has two navigation and editing modes: normal mode, where editing and navigation is performed using the mouse, and cursor mode where editing and navigation are performed using the keyboard. The F2 key is used to switch between these two modes.
+ Jalview has two navigation and editing modes: {\bf normal mode}, where
+ editing and navigation is performed using the mouse, and {\bf cursor mode}
+ where editing and navigation are performed using the keyboard. The {\bf F2 key}
+ is used to switch between these two modes. With a Mac as the F2 is
+ often assigned to screen brightness, one may often need to type {\bf function
+ [Fn] key with F2}.
\begin{figure}[htb]
\begin{center}
\includegraphics[width=6.5in]{images/jalview_anatomy.pdf}
-\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labelled.}
+\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labeled.}
% TODO: modify text labels to be clearer - black on grey and black border for clarity
\label{anatomy}
\end{center}
\end{figure}
-\subsection{Navigation in Normal mode}
+\subsection{Navigation in Normal Mode}
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
$\Rightarrow$ Close All} option from the Jalview desktop.
{\bf \em{Warning: make sure you have saved your work because this cannot be
-undone !}} }
+undone!}} }
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
-\subsection{Navigation in Cursor mode}
+\subsection{Navigation in Cursor Mode}
\label{cursormode}
-\parbox[c]{5in}{Cursor mode navigation enables the experienced user to quickly
+\parbox[c]{5in}{Cursor mode navigation enables the user to quickly
and precisely navigate, select and edit parts of an alignment. On pressing F2 to
enter cursor mode the position of the cursor is indicated by a black background
and white text. The cursor can be placed using the mouse or moved by pressing
Rapid movement to specific positions is accomplished as listed below:
\begin{list}{$\circ$}{}
-\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to move to sequence (row) {\sl n}
+\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to
+move to sequence (row). {\sl n}
\item {\bf Jump to Column {\sl n}:} Type a number {\sl n} then press [C] to move to column {\sl n} in the alignment.
\item {\bf Jump to Residue {\sl n}:} Type a number {\sl n} then press [P] to move to residue number {\sl n} in the current sequence.
\item {\bf Jump to column {\sl m} row {\sl n}:} Type the column number {\sl m}, a comma, the row number {\sl n} and press [RETURN].
\exercise{Navigation}{
\label{navigate}
-\exstep{Reload the example file by accessing the Desktop's
-{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} dialog and
-clicking on the {\sl down arrow} to retrieve the example file URL stored in its history
- (\url{http://www.jalview.org/examples/exampleFile_2_7.jar})}
+Jalview has two navigation and editing modes: {\bf normal} mode (where editing
+and navigation are via the mouse) and the {\bf cursor} mode (where editing and
+navigation are via the keyboard).
+The {\bf F2 key} is used to switch between these two modes. With a Mac often
+need to type function {\bf Fn key and F2}, as button is often assigned to
+screen brightness. Jalview always starts up in {\bf normal mode}.
+
+\exstep{Load an example alignment from its URL
+(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
+using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} dialog
+box.
+(The URL should be stored in its history and clicking on the {\sl down arrow} is
+an easy way to access it.)}
\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
-\exstep{Find and open the Overview Window. Move around the alignment by clicking and dragging the red box in the overview window.}
-\exstep{Look at the status bar as you move the mouse over the alignment. It
-should indicate information about the sequence and residue under the cursor.
-} \exstep{Press [F2] to enter Cursor mode. Use the arrow keys to move the cursor
-around the alignment.
-Move to sequence 7 by pressing {\sl 7 S}. Move to column 18 by pressing {\sl 1 8
-C}. Move to residue 18 by pressing {\sl 1 8 P}. Note that these can be two
-different positions if gaps are inserted into the sequence. Move to sequence 5,
-column 13 by typing {\sl 1 3 , 5 [RETURN]}.
-} }
+\exstep{Find the Overview Window, {\sl Views
+$\Rightarrow$ Overview Window} and open it. Move around the
+alignment by clicking and dragging the red box in the overview window.}
+\exstep{Return to the alignment window. Look at the status bar (lower left hand
+corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
+sequence and residue under the cursor.}
+\exstep{Press [F2] key (or [Fn]/[F2] on Mac) to enter {\bf Cursor mode}. Use
+the direction {\bfarrow keys} to move the cursor around the alignment.}
+\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
+{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
+two different positions if gaps are inserted into the sequence. Move to sequence 5,
+column 13 by typing {\bf 1 3 , 5 [RETURN]}.}
+
+{\bf Note:} To view Jalview's comprehensive on-line help documentations select
+Help on desktop menu, clicking on Documentation will open a Documentation
+window. Select topic from the navigation panel on the left hand side or use the
+Search tab to select specific key words
+
+{\bf Help navigating Jalview is available in a video on
+\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
+the website.}}
+
\subsection{The Find Dialog Box}
\label{searchfunction}
A further option for navigation is to use the {\sl Select $\Rightarrow$
expressions for searching sequences and sequence IDs, or sequence numbers.
Hitting the [Find next] button will highlight the first (or next) occurrence of
that pattern in the sequence ID panel or the alignment, and will adjust the view
-in order to display the highlighted region. The Jalview help provides
+in order to display the highlighted region. The Jalview Help provides
comprehensive documentation for this function, and a quick guide to the regular
expressions that can be used with it.
%TODO insert a figure for the Find dialog box
-\section{Loading your own sequences}
+\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 -
+ 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.
+ 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.
\begin{center}
\includegraphics[width=2in]{images/menuloadurl.pdf}
\includegraphics[width=3in]{images/loadurlbox.pdf}
-\caption{{\bf Opening an alignment from a URL }}
+\caption{{\bf Opening an alignment from a URL. }}
\label{loadurl}
\end{center}
\end{figure}
\begin{center}
\includegraphics[width=2in]{images/menuloadtext.pdf}
\includegraphics[width=3in]{images/loadtextbox.pdf}
-\caption{{\bf Opening an alignment from pasted text }}
+\caption{{\bf Opening an alignment from pasted text. }}
\label{loadtext}
\end{center}
\end{figure}
-\subsection{From a public database}
+\subsection{From a Public Database}
\label{fetchseq}
Jalview can retrieve sequences and sequence alignments from the public databases
housed at the European Bioinformatics Institute, including Uniprot, Pfam, Rfam
registry. Jalview's sequence fetching capabilities allow you to avoid having to
manually locate and save sequences from a web page before loading them into
Jalview. It also allows Jalview to gather additional metadata provided by the
-source, such as annotation and database cross references.
+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}). Pressing the database selection
button in the dialog box opens a new window showing all the database sources
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/fetchseq.pdf}
-\caption{{\bf Retrieving sequences from a public database}}
+\caption{{\bf Retrieving sequences from a public database.}}
\label{loadseq}
\end{center}
\end{figure}
-\exercise{Loading sequences}{
+\exercise{Loading Sequences}{
\label{load}
-\exstep{Start Jalview then close all windows (if necessary) by selecting {\sl Window $\Rightarrow$ Close All} from the Desktop window.}
-\exstep{Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box. Click OK
-and the alignment should load.
-}
-\exstep{Close all windows using the {\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
-
-Point your web browser at the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) 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 Desktop $\Rightarrow$ 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
-URL directly onto Jalview.
-}
-\exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s)..} from the Desktop. Select the PFAM seed database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. }
-\exstep{Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
-web browser.
-
-{\bf Note:} If the URL is downloaded instead of opened in the browser, then locate the file in your download directory and open it in a text editor.
-}
-\exstep{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}.
+\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
+close all windows.}
+\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box.
+
+Click OK to load the alignment.}
+\exstep{{\bf Loading sequences from a file:} Close all windows using the
+{\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
+Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
+your web browser and {\bf save} the file to your desktop.
+
+Open the file you have just saved in Jalview by selecting {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu and
+selecting this file.
+Click OK to load the alignment.}
+\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+
+(i) Select {\sl Desktop $\Rightarrow$ Window
+$\Rightarrow$ Close All}. Then drag the alignment.fa file from the desktop and
+drop it onto the Jalview window, the alignment should open.
+
+Test the differences
+between (a) dragging the sequence onto the empty Jalview desktop and (b)
+dragging the sequence onto an existing alignment window.
+
+(ii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
+web browser. Drag the URL directly from browser window onto Jalview.
+
+(If the URL is downloaded instead of opened in the browser, then
+locate the file in your download directory and open it in a text editor.)
+
+(iii) Open the alignment.fa file using text editor. Copy the sequence text from the
+file into the clipboard and paste it into the desktop
+background by right-clicking and selecting Paste to new alignment option.
+
+(iv) In the text editor, copy the sequence text from
+alignment.fa into the clipboard (usually {\sl via} the browser's {\sl Edit
+$\Rightarrow$ Copy} menu option). In the Desktop menu, 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.}
+\exstep{{\bf Loading sequences from Public Database:} Select {\sl File
+$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
+called New Sequence Fetcher.
+Press database selection button at the top of the dialog box, this opens
+another window called Select Database Retrieval Source showing all the database
+sources.
+
+Select the {\bf PFAM seed} database and click ok, then enter the accession
+number {\bf PF03460} and click OK. An alignment of about 174 sequences should
+load, these can be viewed using the Overview window accessible from {\sl View
+$\Rightarrow$ Overview Window.}.
+
+Several database IDs
+or accession numbers can be loaded by using semicolons to separate them.}}
\subsection{Memory Limits}
\label{memorylimits}
parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
-\section{Writing sequence alignments}
-\label{savingalignments} \subsection{Saving the alignment} Jalview allows the
+\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
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
+jalview format (.jar) is the only format which will preserve the colours,
+groupings and other additional 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
+Unfortunately only Jalview program 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.
%[fig 10]
\parbox[c]{4in}{
\includegraphics[width=4in]{images/saveas2.pdf}
}
-\caption{{\bf Saving alignments in Jalview to disk}}
+\caption{{\bf Saving alignments in Jalview to disk.}}
\label{savealign}
\end{center}
\end{figure}
\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
+\parbox[c]{4in}{If you wish to save a complete Jalview session rather than
+just a single alignment (e.g. because you have calculated trees or multiple
+different alignments) then save your work as a Jalview Project
+file (.jvp).\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
\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}). }
-\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 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 {\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}
+\exstep{Launch Jalview, or use close all windows.
+Load the ferredoxin
+alignment from PFAM (seed) data base using the 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 your preferred format. All
+formats except {\sl Jalview } jvp 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 saving the files in different file formats.}
+\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}.
+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 active in Jalview. Open the
+overview window {\sl View $\Rightarrow$ Overview Window}
+ and scroll red box to any part of the alignment.
+Select {\sl File
+$\Rightarrow$ Save Project} from the main menu and save the project in a
+suitable folder.
+
+Close all windows and then load the project {\sl via} the {\sl File
+$\Rightarrow$ Load Project} menu option. Observe 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.
-\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 $\Rightarrow$ To New Alignment} in the alignment window menu options.
-To clear (unselect) the selection press the [ESC] (escape) key.
+{\bf To clear (unselect) the selection press the [ESC] (escape) key.}
-\subsubsection{Selecting arbitrary regions}
+\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}
\includegraphics[width=4in]{images/select1.pdf}
-\caption{{\bf Selecting a region in an alignment}}
+\caption{{\bf Selecting a region in an alignment.}}
\label{select}
\end{center}
\end{figure}
-\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}).
+\subsubsection{Selecting Columns}
+To select the same residues in all sequences, click and drag along the alignment ruler.
+This selects the entire column of the alignment. Ranges of positions from the
+alignment ruler can also be selected by clicking on the first position and 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]
\end{center}
\end{figure}
-\subsubsection{Selecting sequences}
+\subsubsection{Selecting Sequences}
\begin{figure}[htb]
\begin{center}
\end{figure}
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}).
+sequence ID panel. The same techniques 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}
+\subsubsection{Making Selections in Cursor Mode}
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})
+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.
\includegraphics[width=1.5in]{images/csel2.pdf}
\includegraphics[width=1.5in]{images/csel3.pdf}
\includegraphics[width=1.5in]{images/csel4.pdf}
-\caption{{\bf Making a selection in cursor mode.} Navigate to the top left corner (left), press [Q] (left center), navigate to the bottom right corner (right center) and press [M] (right)}
+\caption{{\bf Making a selection in cursor mode.} Navigate to the top left
+corner (left), press [Q] (left center), navigate to the bottom right corner (right center) and press [M] (right).}
\label{cselect}
\end{center}
\end{figure}
-\subsubsection{Inverting the current selection}
+\subsubsection{Inverting the Current Selection}
The current sequence or column selection can be inverted, using {\sl Select
$\Rightarrow$ Invert Sequence/Column Selection} in the alignment window.
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 }.
+$\Rightarrow$ Selected Region}.
-\subsection{Creating groups}
+\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
\begin{center}
\includegraphics[width=3in]{images/group1.pdf}
\includegraphics[width=1.5in]{images/newgroup.pdf}
-\caption{{\bf Creating a new group from a selection}}
+\caption{{\bf Creating a new group from a selection.}}
\label{makegroup}
\end{center}
\end{figure}
By default the new group will have a box drawn around it. The appearance of the group can be changed (see Section \ref{colours} below). This group will stay defined even when the selection is removed.
-\subsection{Exporting the current selection}
+\subsection{Exporting the Current Selection}
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
Save As } pulldown menu option from the text box.
-\exercise{Making selections and groups}{
+\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.
-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 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 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.}
+\exstep{Close all windows in Jalview.
+Load the ferredoxin alignment (PFAM
+ID PF03460 from PFAM seed database).
+Choose a residue and place the mouse
+cursor on it. Note residue information will show in alignment window status bar.
+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.
+Press [ESC] to clear the selection.}
+\exstep{ Select one sequence by clicking on
+the sequence ID panel. Note that the sequence ID takes on a highlighted
+background and a red box appears around the selected sequence.
+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.
+
+Hold down [CTRL] and then 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{ Select column by clicking on the Alignment Ruler. Note whole
+column is highlighted with a red box.
+Hold down [SHIFT] and click column beyond. Note the selection expands to include
+all the sequences between the two positions on which you clicked.}
+
+\exstep{ To selecting arbitrary regions in alignment, place the mouse at the top
+left corner of the region you wish to select. Press and hold the mouse button.
+Drag the mouse to the bottom right corner of the chosen region and release the
+mouse button and a dashed red box appears around the selected region}
+\exstep{Enter Cursor mode using [F2] (or [Fn]-F2 for Macs).
+Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
+Press {\bf Q} to mark this position.
+Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
+to complete the selection. Note to clear the selection press the {\bf[ESC]}
+key.}
+\exstep{To create a {\bf group} from the selected the region, click the
+right mouse button when mouse is on the selection, this opens a
+pop-up menu in the alignment window.
+
+Open the {\sl Selection $\Rightarrow$ Edit New 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 in
+the alignment by clicking on their Sequence ID label. Note how the group expands
+to include newly selected sequences, and the `Percentage Identity' colouring changes. }
+\exstep{ Another way to resize the group is by using the mouse to click and drag
+the right-hand edge of the selected group.}
+
+\exstep{The current selection can be {\bf exported} and saved by right clicking
+on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
+output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
+\ldots} submenu.
+}
+\exstep{In the alignment output window, try manually editing the alignment,
+importing group into a new alignment window by clicking the [New Window] button to import the
+file into a new alignment window.}
% more? change colouring style. set border colour.
}
-\subsection{Reordering the alignment}
+\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}
-\caption{{\bf Reordering the alignment.} The selected sequence moves up one position on pressing the $\uparrow$ key}
+\caption{{\bf Reordering the alignment.} The selected sequence moves up one
+position on pressing the $\uparrow$ key.}
\label{reorder}
\end{center}
\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. 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.
-}
-}
+\exercise{Reordering the Alignment}{
+\exstep{Close all windows in Jalview from desktop. Load the ferredoxin alignment (e.g.the
+PFAM domain PF03460 from PFAM seed).
+Select one of the sequence in the sequence ID panel, use the up and down
+arrow keys to alter the sequence's position in the alignment. (Note that
+this will not work in cursor mode)}
+\exstep{To select and move multiple
+sequences, use hold [SHIFT] and [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}
+\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 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 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.
+To hide a set of sequences, select them and right-click the mouse on the
+selected sequence IDs to bring up the context pop-up 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 small 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 {\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.
+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 pop-up 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 small 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}
$\Rightarrow$ All but Selected Region } menu entry, or press [Shift]+[Ctrl]+H
to hide the unselected region.
-\subsubsection{Representing a group with a single sequence}
+\subsubsection{Representing a Group with a Single Sequence}
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
-\exercise{Hiding and revealing regions}{
-\exstep{Close all windows then open the PFAM accession PF03460. Select a contiguous set of sequences by clicking and dragging on the sequence ID panel. Right click on the selected sequence IDs and select {\sl Hide Sequences}.
+\exercise{Hiding and Revealing Regions}{
+\exstep{Close all windows, open the PFAM accession PF03460. Select a
+contiguous set of sequences by clicking and dragging on the sequence ID panel.
+Right click on the selected sequence IDs to bring up the sequence ID pop-up
+menu, select {\sl Hide Sequences}.
}
\exstep{
-Right click on the blue triangle indicating hidden sequences and select {\sl Reveal Sequences}. (If you have hidden all sequences then you will need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.})
-}
+Right click on the blue triangle indicating hidden sequences and select {\sl
+Reveal Sequences} in the panel. (If you have hidden all sequences then you will
+need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.}) }
\exstep{
-Repeat but using a non-contiguous set of sequences. Note that when multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
+Repeat the process but use a non-contiguous set of sequences. Note that when
+multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
}
-\exstep{Repeat the above but hiding and revealing columns instead of sequences.
-}
-\exstep{Select a region of the alignment, add in some additional columns to the
-selection, and experiment with the `Hide all but selected region' function. }
-\exstep{Select some sequences and pick one to represent the rest. Bring up the sequence ID pop-up menu for that sequence and select the {\sl Represent group with $<$Sequence ID$>$ } option. Use the pop-up menu again to reveal the hidden sequences that you just picked a representative for.}
+\exstep{Repeat the above using columns to hide and reveal columns
+instead of sequences.
}
+\exstep{Select a region of the alignment, then add in some additional columns to
+the selection, and experiment with the `Hide all but selected region' function
+in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
+\exstep{Select some sequences and pick one to represent the rest by hovering
+the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
+clicking and then select {\sl (Sequence ID name) $\Rightarrow$ Represent group
+with (Sequence ID name )}. To reveal these hidden sequences, right click on the
+Sequence ID and in the pop-up menu select Reveal All.}}
+
+
+\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 while pressing and holding [SHIFT].}
+\label{gapseq}
+\end{center}
+\end{figure}
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit3.pdf}
+\includegraphics[width=3in]{images/edit4.pdf}
+\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
+group is dragged to the right with [CTRL] pressed.}
+\label{gapgroup}
+\end{center}
+\end{figure}
-\subsection{Introducing and removing gaps}
+\subsection{Introducing and Removing Gaps}
The alignment view provides an interactive editing interface, allowing gaps to be inserted or deleted to the left of any position in a sequence or sequence group. Alignment editing can only be performed whilst in keyboard editing mode (entered by pressing [F2]) or by clicking and dragging residues with the mouse when [SHIFT] or [CTRL] is held down (which differs from earlier versions of Jalview).
\subsubsection{Locked Editing}
\label{lockededits}
The Jalview alignment editing model is different to that used in other alignment
-editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, but does not avoid the `knock-on' effect which is sometimes undesirable. However, its effect can be limited by performing the edit within a selected region. In this case, gaps will only be removed or inserted within the selected region. Edits are similarly constrained when they occur adjacent to a hidden column.
+editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position,
+editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of
+alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment,
+but does not avoid the `knock-on' effect which is sometimes undesirable.
+However, its effect can be limited by performing the edit within a selected region.
+In this case, gaps will only be removed or inserted within the selected region.
+Edits are similarly constrained when they occur adjacent to a hidden column.
-\subsubsection{Introducing gaps in a single sequence}
+\subsubsection{Introducing Gaps in a Single Sequence}
-To introduce a gap, place the cursor on the residue to the immediate right of where the gap should appear. Hold down the SHIFT key and the left mouse button, then drag the sequence to the right till the required number of gaps has been inserted.
+To introduce a gap, first select the sequence in the sequence ID panel and
+then place the cursor on the residue to the immediate right of where the gap
+should appear. Hold down the SHIFT key and the left mouse button, then drag the sequence to the right until the required number of gaps has been inserted.
One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
-\subsubsection{Introducing gaps in all sequences of a group}
+\subsubsection{Introducing Gaps in all Sequences of a Group}
-To insert gaps in all sequences in a selection or group, place the mouse cursor on any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
+To insert gaps in all sequences in a selection or group, select the
+required sequences in the sequence ID panel and then place the mouse cursor on
+any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
Gaps can be removed by dragging the residue to the immediate right of the gap
leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences).
\subsubsection{Sliding Sequences}
Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the selected sequences to the left or
-right (respectively). Slides occur regardless of the region selection -
+sequences are selected will ``slide'' the entire selected sequences to the left
+or right (respectively). Slides occur regardless of the region selection -
which, for example, allows you to easily reposition misaligned subfamilies
within a larger alignment.
-\subsubsection{Undoing edits}
+\subsubsection{Undoing Edits}
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
% % better idea to introduce hiding sequences, and use the invert selection, hide
% others, to simplify manual alignment construction
-\exercise{Editing alignments}{
+\exercise{Editing Alignments}{
\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{You are going to manually reconstruct part of the example Jalview alignment
}
\exstep{ Select the first 7 sequences, and press H to hide them (or right click
-on the sequence IDs to open the sequence ID popup menu, and select {\sl Hide
+on the sequence IDs to open the sequence ID pop-up menu, and select {\sl Hide
Sequences}). }
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
-the left so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
+the right 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: you can do this by pressing [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.}
\exstep{ Select all the visible
-sequences in the block by pressing [CTRL]-A. Insert a single gap in all selected
-sequences at column 38 by holding [CTRL] and clicking on the R in FER1\_SPIOL and
-dragging one column to right. Insert another gap at column 47 in all sequences in
-the same way.}
+sequences (those not hidden) in the block by pressing [CTRL]-A.
+
+Insert a single
+gap in all selected sequences at column 38 of the alignment by holding [CTRL]
+and clicking on the R at column 38 in the FER1\_SPIOL, then drag one
+column to right.
+Insert another gap at column 47 in all sequences in the same way.}
\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
inserting two additional gaps after the gap at column 47: First press [ESC] to
\exstep{ Now complete the
alignment of FER1\_SPIOL with a {\bf locked edit} by pressing [ESC] and select
columns 47 to 57 of the FER1\_SPIOL row. Move the mouse onto the G at column 50,
-hold [SHIFT] and drag the G to the left by one column to insert a gap at column
-57.}
+hold [SHIFT] and drag the G in column 47 of FER1\_SPIOL to the left by one
+column to insert a gap at column 57.}
\exstep{ In the next two steps you will complete the alignment of the last two sequences.
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
+so it lies at column 10.
+
+Keep holding [SHIFT] and click and drag to insert
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).}
}
-\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 while pressing and holding [SHIFT].}
-\label{gapseq}
-\end{center}
-\end{figure}
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit3.pdf}
-\includegraphics[width=3in]{images/edit4.pdf}
-\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
-group is dragged to the right with [CTRL] pressed.}
-\label{gapgroup}
-\end{center}
-\end{figure}
-
-
\subsubsection{Editing in Cursor mode}
-Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by
+Gaps can 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]
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
+\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.
-{\bf {\sl Note for Windows Users:}} The [SHIFT]-[SPACE] command has the same effect as
-the [CTRL]-[SPACE] command mentioned in this exercise, and you should use
-[SHIFT]-[SPACE] in order to avoid opening the window menu.}
+{{\bf Note:}} For Mac users, [CTRL]-[SPACE] command
+has the same effect as the [SHIFT]-[SPACE] command mentioned in this exercise.
+
+Window users should use [SHIFT]-[SPACE] rather than the [CTRL]-[SPACE] command,
+as this command will close the window.}
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
Now, enter cursor mode by pressing [F2]}
% 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 {\sl [CTRL]} and press {\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 press {\sl [RETURN]}. Now insert 6 gaps in all the sequences.
+Type {\sl 6} then hold down {\sl [SHIFT]} 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.}
+Press {\sl 34C} then {\sl [SHIFT]-[SPACE]}. Press {\sl 38C} then
+[SHIFT]-[SPACE].
+Press {\sl 47C} then {\sl 3 [SHIFT-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.}
}
-\section{Colouring sequences}
+\section{Colouring Sequences}
\label{colours}
Colouring sequences is a key aspect of alignment presentation. Jalview allows
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Features} option before you can see your colourscheme.
-There are two main types of colouring styles: simple static residue colourschemes and dynamic schemes which use conservation and consensus analysis to control colouring. A hybrid colouring is also possible, where static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
+There are two main types of colouring styles: {\bf simple static residue}
+colourschemes and {\bf dynamic schemes} which use conservation and consensus
+analysis to control colouring. {\bf Hybrid colouring} is also possible, where
+static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
-\subsection{Colouring the whole alignment}
+\subsection{Colouring the Whole Alignment}
\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.
}
}
-\subsection{Colouring a group or selection}
+\subsection{Colouring a Group or Selection}
-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.
+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}). This only changes the colour of the current selection or group.
+The second method is to select sequences and right click mouse to open pop-up
+menu and select {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group
+Colour} from context menu options
+(Figure \ref{colgrp}). This only changes the colour of the current selection or group.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsection{Shading by conservation}
+\subsection{Shading by Conservation}
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
\end{center}
\end{figure}
-\subsection{Thresholding by percentage identity}
+\subsection{Thresholding by Percentage Identity}
`Thresholding' is another hybrid colour model where a residue is only coloured
if it is not excluded by an applied threshold. Selecting {\sl Colour $\Rightarrow$ Above Identity Threshold} brings up a selection box with a slider controlling the minimum percentage identity threshold to be applied. Selecting a higher threshold (by sliding to the right) limits the colouring to columns with a higher percentage identity (as shown by the Consensus histogram in the annotation panel).
}\parbox[c]{3in}{
\centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
-The {\bf per Sequency only} option in the {\bf Colour By Annotation} dialog
+The {\bf per Sequence} option in the {\bf Colour By Annotation} dialog
allows each sequence to be shaded according to sequence associated annotation
-rows, such as protein disorder scores. This functionality is described futher in
-Section \ref{protdisorderpred}.
+rows, such as protein disorder scores. This functionality is described further
+in Section \ref{protdisorderpred}.
-\subsection{Colour schemes}
+\subsection{Colour Schemes}
\label{colscheme}
Full details on each colour scheme can be found in the Jalview on-line help. A brief description of each one is provided below:
\subsubsection{Taylor}
\parbox[c]{3.5in}{
-This colour scheme was devised by Willie Taylor and an entertaining description of it's origin can be found in Protein Engineering, Vol 10 , 743-746 (1997)
+This colour scheme was devised by Willie Taylor and an entertaining description of its origin can be found in Protein Engineering,
+Vol 10 , 743-746 (1997).
}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_taylor.pdf}
\parbox[c]{3.5in}{ Residues are coloured according to whether the corresponding
nucleotide bases are purine (magenta) or pyrimidine (cyan) based. All non ACTG
residues are uncoloured. For further information about working with nucleic acid
-sequences and alignments, see Section \ref{workingwithnuc}
+sequences and alignments, see Section \ref{workingwithnuc}.
%and Section \ref{workingwithrna}
-.
} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_purpyr.pdf} }
-\subsubsection{RNA Helix colouring}
+\subsubsection{RNA Helix Colouring}
\parbox[c]{3.5in}{ Columns are coloured according to their assigned RNA helix as
defined by a secondary structure annotation line on the alignment. Colours for
each helix are randomly assigned, and option only available when an RNA
\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
\exercise{Colouring Alignments}{
+\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected
+in View sequence alignment menu.
+ This must be turned {\sl off} specifically as it is {\sl on} by default.}
\exstep{
-Open a sequence alignment, for example the PFAM domain PF03460. Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
+Open a sequence alignment, for example the PFAM domain PF03460 in PFAM seed.
+Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
}
\exstep{
-Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in exercise \ref{exselectgrpcolour} during the group selection step).
+Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group
+of around 4 similar sequences. Use the context menu (right click on the group)
+option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
+$\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which
+were not coloured are now coloured. The calculations performed for dynamic
+colouring schemes like Blosum62 are based on the group being coloured, not the
+whole alignment (this also explains the colouring changes observed in exercise
+\ref{exselect} during the group selection step).
}
\exstep{
-Keeping the same selection as before, colour the complete alignment using {\sl Colour $\Rightarrow$ Taylor}. Select the menu option {\sl Colour $\Rightarrow$ By Conservation}. Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
+Keeping the same selection as before, colour the complete alignment except
+the group using {\sl Colour $\Rightarrow$ Taylor}.
+Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
+Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
}
}
\end{figure}
-\exercise{User defined colour schemes}{
+\exercise{User Defined Colour Schemes}{
\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.
}
\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.
}
}
-\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 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 outputted in an
+exported graphics file.
+It is therefore important to pick the right kind of display layout prior to generating figures.
\subsection{Multiple Alignment Views}
% JBPNote make an excercise on views ?
-\subsection{Alignment layout}
+\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}
+\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.
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{center}
\parbox[c]{2in}{\includegraphics[width=2in]{images/wrap1.pdf}}
\parbox[c]{4in}{\includegraphics[width=4in]{images/wrap2.pdf}}
-\caption{{\bf Wrapping the alignment}}
+\caption{{\bf Wrapping the alignment.}}
\label{wrap}
\end{center}
\end{figure}
\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}
+\subsubsection{Numbering and Label Justification}
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}
+\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}
+\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 Selection $\Rightarrow$ Group
display gaps or sequence symbols that differ from the consensus for each
column, and render all others with a `.'.
%TODO add a graphic to illustrate this.
-\subsection{Annotation ordering and display}
+\subsection{Annotation Ordering and Display}
% 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{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 {\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
+can be hidden and revealed in the same way as sequences {\sl via} the
+pop-up 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 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{center}
\includegraphics[width=2.5in]{images/annot1.pdf}
\includegraphics[width=2.5in]{images/annot2.pdf}
-\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl View} menu (left) or individually from the context menu (right)}
+\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl
+View} menu (left) or individually from the context menu (right).}
\label{annot}
\end{center}
\end{figure}
\exercise{Alignment Layout}{
\label{exscreen}
-\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}. Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. Experiment with the various options from the {\sl Format} menu. to adjust the ruler placement, sequence ID format and so on. }
-\exstep{Hide all the annotation rows by selecting {\sl View $\Rightarrow$ Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.}
-\exstep{{\bf Deselect} {\sl Format $\Rightarrow$ Wrap}, and right click on the annotation row labels to bring up the context menu. Select {\sl Hide This Row}. Bring up the context menu again and select {\sl Show All Hidden Rows} to reveal them}
+\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}.
+Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
+Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
+sequence ID format and so on. }
+\exstep{Hide all the annotation rows by selecting {\sl Annotations $\Rightarrow$
+Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} \exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
+annotation row labels to bring up the pop-up context menu, then select {\sl
+Hide This Row}. Bring up the pop-up context menu again and select {\sl
+Show All Hidden Rows} to reveal them.}
\exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot} below.}
-\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label - a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed by Clicking and dragging the mouse up or down.}
+\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label -
+a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
+by clicking and dragging the mouse up or down.}
}
-\subsection{Graphical output}
+\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 {\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}}}
}
\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 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{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 favoured web browser. }
+\exstep{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 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
available to Jalview users, and Section \ref{jabaservices} explains how to
configure the Jalview Desktop for access to new JABAWS servers.
Section \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS' AACon
+programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS AACon
service for protein multiple alignment conservation analysis.
Section \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS' protein disorder prediction
+structure predictions with JPred, and JABAWS protein disorder prediction
services are introduced in Section \ref{protdisorderpred}.
Section \ref{featannot} describes the mechanisms provided by Jalview for
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
-\section{Working with structures}
+\section{Working with Structures}
\label{wkwithstructure}
Jalview facilitates the use of protein structures for the analysis of alignments
by providing a linked view of structures associated with sequences in
the European Protein Databank (PDBe) using the Sequence Fetcher (see
\ref{fetchseq}).
-\subsection{Automatic association of PDB structures with sequences}
+\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}
+\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
}
}
-\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence. After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and any associated PDB structures (right)}
+\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence.
+After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and
+any associated PDB structures (right).}
\label{auto}
\end{center}
\end{figure}
-\subsubsection{Drag-and-drop association of PDB files with sequences by filename
-match}
+\subsubsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
+Match}
\label{multipdbfileassoc}
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
If no associations are made, then sequences extracted
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
+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 already collected in a directory
accessible from your computer.\footnote{We plan to extend this facility in
\subsection{Viewing Structures}
+\label{viewAllStructures}
The structure viewer can be launched in two ways from the sequence ID context
menu. To view a particular structure associated with a sequence in the
alignment, simply select it from popup menu's associated structures submenu in
\end{center}
\end{figure}
-\subsection{Customising structure display}
+\subsection{Customising Structure Display}
Structure display can be modified using the {\sl Colour} and {\sl View} menus
in the structure viewer. The background colour can be modified by selecting 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.
-\subsubsection{Using the Jmol visualization interface }
+\subsubsection{Using the Jmol Visualization Interface }
Jmol has a comprehensive set of selection and visualization functions that are
accessed from the Jmol popup menu (by right-clicking in the Jmol window or by
Verify that the Jmol display is as it was when you just saved the file.}
}
-\subsection{Superimposing structures}
+\subsection{Superimposing Structures}
\label{superposestructs}
Many comparative biomolecular analysis investigations aim to determine if the
biochemical properties of a given molecule are significantly different to its
$>$ 1) if the current selection contains two or more sequences with associated
structures.
-\subsubsection{Obtaining the RMSD for a superposition}
+\subsubsection{Obtaining the RMSD for a Superposition}
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
$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
includes 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
+\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 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.
\end{center}
\end{figure}
-\exercise{Aligning structures using the ferredoxin
-sequence alignment.}{\label{superpositionex}
+\exercise{Aligning Structures using the Ferredoxin
+Sequence Alignment}{\label{superpositionex}
\exstep{Continue with the Jalview project created in exercise
\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
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}
-Normally, the original view from which a particular structure view was
+\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
\end{center}
\end{figure}
-\subsubsection{Colouring complexes}
+\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
The ability to control which multiple alignment view is used to colour
structural data is essential when working with data relating to
evolutionary history, and a complete picture of functional variation can
only be gained by integrating data from different alignments on the same
structure view. An example of this is shown in Figure
-\ref{mviewalcomplex}, based on data from Song et. al\footnote{Structure of
+\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} 2011 {\bf 331} 1036-1040
\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
\end{center}
\end{figure}
-\exercise{Colouring a protein complex to explore domain-domain interfaces}{\label{dnmtcomplexex}
+\exercise{Colouring a Protein Complex to Explore Domain-Domain
+Interfaces}{\label{dnmtcomplexex}
\exstep{Download the PDB file at
-\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. This
-is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA server.}
+\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
+
+This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
+server.}
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
free memory available.
{\sl Use the following webstart link:
-\href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}}.}
+
+\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}}
\exstep{Retrieve the following
{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
\exstep{Drag the structure you downloaded in
in the structure.}}
\exstep{Save your work as a Jalview project and verify that it can be opened again by starting another Jalview Desktop instance, and dragging the saved project into the desktop window.}
-{\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
-you notice any strange behaviour when trying out this exercise, it may be a
-bug (see
-\href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
-for one relating to highlighting of positions in the alignment window).} }
+% {\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
+% you notice any strange behaviour when trying out this exercise, it may be a
+% bug (see
+% \href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
+% for one relating to highlighting of positions in the alignment window).}
+}
-\section{Analysis of alignments}
+\section{Analysis of Alignments}
\label{alignanalysis}
Jalview provides support for sequence analysis in two ways. A number of
analytical methods are `built-in', these are accessed from the {\sl Calculate}
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\includegraphics[width=3in]{images/PCA3.pdf}
-\caption{{\bf PCA Analysis} }
+\caption{{\bf PCA Analysis.} }
\label{PCA}
\end{center}
\end{figure}
the partitioned tree and the points in the PCA plot.
} }
-\subsubsection{PCA data export}
+\subsubsection{PCA Data Export}
Although the PCA viewer supports export of the current view, the plots produced
are rarely suitable for direct publication. The PCA viewer's {\sl File} menu
includes a number of options for exporting the PCA matrix and transformed points
\includegraphics[width=2.5in]{images/trees1.pdf}
\includegraphics[width=2.5in]{images/trees2.pdf}
\includegraphics[width=1.25in]{images/trees4.pdf}
-\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees. Jalview can also load precalculated trees in Newick format (right).}
+\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees.
+Jalview can also load precalculated trees in Newick format (right).}
\label{trees1}
\end{center}
\end{figure}
\begin{figure}
\begin{center}
\includegraphics[width=5in]{images/trees3.pdf}
-\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate groups in Jalview}
+\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
+groups in Jalview.}
\label{trees2}
\end{center}
\end{figure}
% move to ch. 3 ?
%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
-\subsubsection{Recovering input data for a tree or PCA plot calculation}
+\subsubsection{Recovering input Data for a Tree or PCA Plot Calculation}
\parbox[c]{5in}{
The {\sl File $\Rightarrow$ Input Data } option will open a new alignment window containing the original data used to calculate the tree or PCA plot (if available). This function is useful when a tree has been created and then the alignment subsequently changed.
}
\parbox[c]{1.25in}{\centerline{\includegraphics[width=1.25in]{images/pca_fmenu.pdf}
}}
-\subsubsection{Changing the associated view for a tree or PCA viewer}
+\subsubsection{Changing the associated View for a Tree or PCA Viewer}
\parbox[c]{4in}{
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{
\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}).}
+\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}).}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
\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.}
\caption{The Redundancy Removal dialog box opened from the edit menu. Sequences that exceed the current percentage identity threshold and are to be removed are highlighted in black.}
\end{figure}
-\exercise{Remove redundant sequences}{
-
-{\sl Note: Jalview 2.8 users - bugs in this version mean that the 'Unlinked leaves' markings will not be shown when sequences are removed during this exercise.}
+\exercise{Remove Redundant Sequences}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
\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.}
}
-\subsection{Subdividing the alignment according to specific mutations}
+\subsection{Subdividing the Alignment According to Specific Mutations}
It is often necessary to explore variations in an alignment that may correlate
with mutations observed in a particular region; for example, sites exhibiting
colourschemes can then be used to reveal any associated pattern of sequence
variation across the whole alignment.
-\subsection{Automated annotation of Alignments and Groups}
+\subsection{Automated Annotation of Alignments and Groups}
On loading a sequence alignment, Jalview will normally\footnote{Automatic
annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
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}{
+\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
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,
+There are two types of one way service in Jalview. Database services,
which were introduced in in Section \ref{fetchseq}, provide sequence and
alignment data. They can also be used to add sequence IDs to an alignment
imported from a local file, prior to further annotation retrieval, as described
in Section \ref{featuresfromdb}. A second type of one way service is provided
by Jalview's DAS sequence feature retrieval system, which is described
-in Section \ref{dasfretrieval}. The final type of one way service are sequence
-and ID submission services, exemplified by the `Envision2 Services' provided
-by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
-INtegration. Please see http://www.enfin.org for more information. }.
-
-\subsubsection{One-way submission services}
-Jalview can use the system's web browser to submit sets of sequences and
-sequence IDs to web based applications. Single sequence IDs can be passed to
-a web site using the user definable URL links listed under the {\sl
-Links} submenu of the sequence ID popup menu. These are configured
-in the {\sl Connections} tab of the {\sl Preferences} dialog box.
-
-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
-the Envision2 web application. The menu entries and their tooltips provide
-details of the Envision2 workflow and the dataset set that will be submitted
-({\sl i.e.} the database reference type, or associated sequence subset). Please
-note, due to technical limitations, Jalview can currently only submit small
-numbers of sequences to the workflows - if no sequence or ID submissions are
-presented in the submenus, then try to select a smaller number of sequences to
-submit.
+in Section \ref{dasfretrieval}.
+% The final type of one way service are sequence
+% and ID submission services.
+% exemplified by the `Envision2 Services' provided
+% by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
+% INtegration. Please see http://www.enfin.org for more information. }.
+
+% \subsubsection{One-way submission services}
+% Jalview can use the system's web browser to submit sets of sequences and
+% sequence IDs to web based applications. Single sequence IDs can be passed to
+% a web site using the user definable URL links listed under the {\sl
+% Links} submenu of the sequence ID popup menu. These are configured
+% in the {\sl Connections} tab of the {\sl Preferences} dialog box.
+%
+% 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
+% the Envision2 web application. The menu entries and their tooltips provide
+% details of the Envision2 workflow and the dataset set that will be submitted
+% ({\sl i.e.} the database reference type, or associated sequence subset). Please
+% note, due to technical limitations, Jalview can currently only submit small
+% numbers of sequences to the workflows - if no sequence or ID submissions are
+% presented in the submenus, then try to select a smaller number of sequences to
+% submit.
\subsection{Remote Analysis Web Services}
Remote analysis services enable Jalview to use external computational
progress of running jobs.
-\subsection{JABA Web Services for sequence alignment and analysis}
+\subsection{JABA Web Services for Sequence Alignment and Analysis}
\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
%%\item Learn how to install JABA services and configure Jalview to access them
%%\end{list}
-\subsection{Changing the Web Services menu layout}
+\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
\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 windowÔøΩs {\sl Web Service} 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 {\sl Enable JABAWS services} checkbox is selected, and unselect
the {\sl Enable Enfin Services} checkboxes.}
Test results from JABAWS are reported on Jalview's console output (opened from
the Tools menu). Tests are re-run every time Jalview starts, and when the
-[Refresh] button is pressed on the Jalview JABAWS configuration panel.
+[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.
-\subsubsection{Resetting the JABA services setting to their defaults}
+\subsubsection{Resetting the JABA Services Setting to their Defaults}
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
`Reset Services' button on the Web Services preferences panel.
-\subsection{Running your own JABA server}
+\subsection{Running your own JABA Server}
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}.
-\exercise{Installing a JABA Virtual Machine on your computer}{
+\exercise{Installing a JABA Virtual Machine on your Computer}{
\label{jabawsvmex}{\sl This tutorial will demonstrate the simplest way of
installing JABA on your computer, and configuring Jalview so it can access the JABA services.
this will begin with `http:' and end with `/jabaws''.}
}
-\exercise{Configuring Jalview to access your new JABAWS virtual appliance}{
+\exercise{Configuring Jalview to Access your new JABAWS Virtual Appliance}{
\label{confnewjabawsappl}
\exstep{Start Jalview (If you have not done so already).}
\exstep{Enable the Jalview Java Console by selecting its option from the Tools
\parbox[c]{2in}{\includegraphics[width=2in]{images/ws3.pdf}}
\caption{{\bf Multiple alignment via web services} The appropriate method is
selected from the menu (left), a status box appears (centre), and the results
-appear in a new window (right)}
+appear in a new window (right).}
\label{webservices}
\end{center}
\end{figure}
provided by ClustalW in this case is effectively a simple form of profile
alignment.
-\subsubsection{Alignments of sequences that include hidden regions}
+\subsubsection{Alignments of Sequences that include Hidden Regions}
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}.
}
-\subsection{Customising the parameters used for alignment}
+\subsection{Customising the Parameters used for Alignment}
JABA web services allow you to vary the parameters used when performing a
bioinformatics analysis. For JABA alignment services, this means you are
\end{list}
-\subsubsection{Getting help on the parameters for a service}
+\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
+Jalview will display as a tooltip, or as a text pane that can be opened under
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
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 Huge
+\item Large alignments (balanced)
\item Protein alignments (fastest speed)
\item Nucleotide alignments (fastest speed)
\end{list}
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 `{\sl Edit settings and run ...}' option from the web serviceÔøΩs menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web services 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.
can handle, then an error message will be shown informing you of the maximum
number allowed by the server.
-\subsection{User defined Presets}
+\subsection{User Defined Presets}
Jalview allows you to create your own presets for a particular service. To do
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
\label{jwsparamsdialog} }
\end{figure}
-\subsubsection{Saving parameter sets}
+\subsubsection{Saving Parameter Sets}
When creating a custom parameter set, you will be asked for a file name to save
it. The location of the file is recorded in the Jalview user preferences in the
same way as a custom alignment colourscheme, so when Jalview is launched again,
% }
% }
-\section{Protein alignment conservation analysis}
+\section{Protein Alignment Conservation Analysis}
\label{aacons}
The {\sl Web Service $\Rightarrow$ Conservation} menu controls the computation
of up to 17 different amino acid conservation measures for the current alignment
score developed by Manning et al. in 2008.\footnote{SMERFS Score Manning et al. {\sl BMC
Bioinformatics} 2008, {\bf 9} 51 \href{http://dx.doi.org/10.1186/1471-2105-9-51}{doi:10.1186/1471-2105-9-51}}
-\subsubsection{Enabling and disabling AACon calculations}
+\subsubsection{Enabling and Disabling AACon Calculations}
When the AACon Calculation entry in the {\sl Web Services $\Rightarrow$
Conservation} menu is ticked, AACon calculations will be performed every time
the alignment is modified. Selecting the menu item will enable or disable
automatic recalculation.
-\subsubsection{Configuring which AACon calculations are performed}
+\subsubsection{Configuring which AACon Calculations are Performed}
The {\sl Web Services $\Rightarrow$ Conservation $\Rightarrow$ Change AACon
Settings ...} menu entry will open a web services parameter dialog for the
currently configured AACon server. Standard presets are provided for quick and
AACon settings for an alignment are saved in Jalview projects along with the
latest calculation results.
-\subsubsection{Changing the server used for AACon calculations}
+\subsubsection{Changing the Server used for AACon Calculations}
If you are working with alignments too large to analyse with the public JABAWS
server, then you will most likely have already configured additional JABAWS
servers. By default, Jalview will chose the first AACon service available from
{\sl Note: you may want to keep this data for use in exercise \ref{viewannotfileex}.}
}
-}
+\exstep{
+In the original alignment that you loaded in step 1, {\bf select all} sequences,
+then open the {\bf Sequence ID $\Rightarrow$ Selection } submenu and select the
+{\bf Add Reference Annotation} option.
+
+The JNet predictions for the sequences should now be visible in the original
+alignment.} }
\section{Protein Disorder Prediction}
\label{protdisorderpred}
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
-\subsection{Disorder prediction results}
+\subsection{Disorder Prediction Results}
Each service operates on sequences in the alignment to identify regions likely
to be unstructured or flexible, or alternately, fold to form globular domains.
As a consequence, disorder predictor results include both sequence features and
\end{center}
\end{figure}
-\subsubsection{Navigating large sets of disorder predictions}
+\subsubsection{Navigating Large Sets of Disorder Predictions}
{\bf Figure \ref{alignmentdisorderannot}} shows a single sequence annotated with
a range of disorder predictions. Disorder prediction annotation rows are
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/disorderpredannot.pdf}
-\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disorderd regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
+\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A
+zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disordered regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
\label{alignmentdisorderannot}
\end{center}
\end{figure}
-\subsection{Disorder predictors provided by JABAWS 2.0}
+\subsection{Disorder Predictors provided by JABAWS 2.0}
For full details of each predictor and the results that Jalview can display,
please consult
\href{http://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's
by default, but can be shown by right-clicking on the alignment
annotation panel and selecting \textbf{Show hidden annotation}.
+\exercise{Protein Disorder Prediction}{
+\label{protdispredex}
+
+\exstep{Open the alignment at
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
+
+\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services
+$\Rightarrow$ Disorder Prediction } submenu.}
+
+\exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
+IDs} to retrieve all the PDB structures for the sequences.}
+
+\exstep{Open and align
+the structures for all sequences.
+
+{\sl Hint: see \ref{viewAllStructures} to see how to do this.}}
+
+\exstep{Compare the disorder predictions to the structure data by mapping any
+available temperature factors to the alignment {\sl via} the {\sl Sequence ID
+Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
+
+\exstep{Apply the IUPred disorder prediction method}
+\exstep{Use the {\sl Per
+sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
+the sequences by the long and short disorder predictors.
+Do the two methods agree with the structure ?}}
+
\section{Features and Annotation}
\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.
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}
+\subsection{Creating Sequence Features}
Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialogue box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
\begin{figure}[htbp]
\end{center}
\end{figure}
-Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence. Each feature remains associated with it's own sequence.
+Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence.
+Each feature remains associated with its own sequence.
-\subsection{Customising feature display}
+\subsection{Customising Feature Display}
Feature display can be toggled on or off by selecting the {\sl View
$\Rightarrow$ Show Sequence Features} menu option. When multiple features are
Features file format for the import of sequence annotation. Features and
alignment annotation are also extracted from other formats such as Stockholm,
and AMSA. URL links may also be attached to features. See the online
-documentation for more details of the additional capabilities of the jalview
+documentation for more details of the additional capabilities of the Jalview
features file.
-\exercise{Creating features}{
+\exercise{Creating Features}{
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in iron binding so we will create them as features. Navigate to column 97, sequence 1. Select the entire column by clicking in the ruler bar. Then right-click on the selection to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}. A dialogue box will appear.
}
\exstep{
now displayed. Close the sequence feature settings box by clicking OK or
Cancel.} }
-\subsection{Creating user defined annotation}
+\subsection{Creating User Defined Annotation}
Annotations are properties that apply to the alignment as a whole and are visualized on rows in the annotation panel.
To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}). A dialogue box appears. Enter the label to use for this row and a new row will appear.
\end{center}
\end{figure}
-\exercise{Annotating alignments}{
+\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 OK. A new, empty, row appears.
}
\exstep{
\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. } }
-\section{Importing features from databases}
+\section{Importing Features from Databases}
\label{featuresfromdb}
Jalview supports feature retrieval from public databases either directly or {\sl
via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}).
-It includes built in parsers for Uniprot and EMBL records retrieved from the
-EBI. Sequences retrieved from these sources using the sequence fetcher (see
+It includes built in parsers for Uniprot and ENA (or EMBL) records retrieved
+from the EBI. Sequences retrieved from these sources using the sequence fetcher (see
Section \ref{fetchseq}) will already possess features.
\subsection{Sequence Database Reference Retrieval}
do not match the coordinate system from which the features were defined, then
the features will be displayed incorrectly.
-\subsubsection{Viewing and exporting a sequence's database annotation}
+\subsubsection{Viewing and Exporting a Sequence's Database Annotation}
You can export all the database cross references and annotation terms shown in
the sequence ID tooltip for a sequence by right-clicking and selecting the {\sl
\parbox[c]{3in}{
\centerline{\includegraphics[width=2.2in]{images/seqdetailsreport.pdf}}}
-\subsubsection{Automatically discovering a sequence's database references}
+\subsubsection{Automatically Discovering a Sequence's Database References}
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
Following DAS feature retrieval, the {\sl Feature Settings} panel takes on a
slightly different appearance (Figure \ref{das} (right)). Each data source is
listed and groups of features from one data source can be selected/deselected
-by checking the labeled box at the top of the panel.
+by checking the labelled box at the top of the panel.
-\subsubsection{The Fetch Uniprot IDs dialog box}
+\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 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}
+\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}{
+\exercise{Retrieving Features with DAS}{
\label{dasfeatretrexcercise}
\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. }
+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.
+A window may prompt whether you wish Jalview to fetch DAS features. 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{
}
}
-\subsection{Colouring features by score or description
-text}
+\subsection{Colouring Features by Score or Description
+Text}
\label{featureschemes}
Sometimes, you may need to visualize the differences in information carried by
sequence features of the same type. This is most often the case when features
style and a greater than ($>$) or less than ($<$) symbol to indicate when a
threshold has been defined.
-\subsection{Using features to re-order the alignment}
+\subsection{Using Features to Re-order the Alignment}
\label{featureordering}
The presence of sequence features on certain sequences or in a particular
region of an alignment can quantitatively identify important trends in
then only features found in that region of the alignment will be used to
create the new alignment ordering.
-\exercise{Shading and sorting alignments using sequence features}{
-\label{shadingorderingfeatsex}
-\exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
-}
-\exstep{Open the
-feature settings panel, and, after first clearing the current
-selection, press the {\em Seq Sort by Density} button a few times.}
-\exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
-scores for the protein sequences in the alignment.
-{\sl Hint: the nickname for the das source is `KD$\_$hydrophobicity'.}}
-\exstep{Change the feature settings so only the hydrophobicity features are
-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 {\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.}
-\exstep{Save the alignment as a project, for use in exercise
-\ref{threshgradfeaturesex}.} }
-
-\exercise{Shading alignments with combinations of graduated feature
-colourschemes}{
-\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 {\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
-({\em hint - there is a switch on the dialog to do this for you}).}
-\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 {\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 and GFF file formats, to see how the different types of graduated feature
-colour styles are encoded. }
-}
+% \exercise{Shading and Sorting Alignments using Sequence Features}{
+% \label{shadingorderingfeatsex}
+%
+% This exercise is currently not included in the tutorial because no DAS servers
+% currently exist that yield per-residue features for any Uniprot sequence.
+%
+% \exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
+% }
+% \exstep{Open the
+% feature settings panel, and, after first clearing the current
+% selection, press the {\em Seq Sort by Density} button a few times.}
+% \exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
+% scores for the protein sequences in the alignment.
+% {\sl Hint: the nickname for the das source is `KD$\_$hydrophobicity'.}}
+% \exstep{Change the feature settings so only the hydrophobicity features are
+% 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 {\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.}
+% \exstep{Save the alignment as a project, for use in exercise
+% \ref{threshgradfeaturesex}.} }
+%
+% \exercise{Shading alignments with combinations of graduated feature
+% colourschemes}{
+% \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 {\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
+% ({\em hint - there is a switch on the dialog to do this for you}).}
+% \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 {\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 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
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
-nucleotide sequence. Mappings are used to to transfer annotation between
+nucleotide sequence. Mappings are used to transfer annotation between
nucleic acid and protein sequences, and to dynamically highlight regions in
one sequence that correspond to the position of the mouse pointer in another.
%TODO Working with Nucleic acid sequences and structures.
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.
-
+sequences (but will be providing services for this in the future!)
\begin{table}{}
\centering
\begin{tabular}{|l|c|l|}
}
-\subsection{Coding regions from EMBL records}
+\subsection{Coding Regions from EMBL Records}
Many EMBL records that can be retrieved with the sequence fetcher contain exons.
Coding regions will be marked as features on the EMBL nucleotide sequence, and
\subsubsection{Retrieval of Protein or DNA Cross References}
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}
+\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 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.
\end{center}
\end{figure}
-\exercise{Visualizing protein features on coding regions}
+\exercise{Visualizing Protein Features on Coding Regions}
{
-\exstep{Use the sequence fetcher to retrieve EMBL record V00488.}
+\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
\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 {\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{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for D49489 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 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}
+\subsection{Working with RNA}
+Jalview allows the creation of RNA secondary structure annotation, and includes
+the VARNA secondary structure viewer for the display of RNA base pair diagrams.
+It also allows the extraction of RNA secondary structure from 3D data when
+available.
+
+\subsection{Performing RNA Secondary Structure Predictions}
+Secondary structure consensus calculations can be performed by enabling the
+VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+Structure} menu. These consensus structures are created by analysing the
+covariation patterns in all visible sequences on the alignment. For more
+information see the VIENNA documentation.
+
+\begin{figure}[htbp]
+\begin{center}
+\label{rnaviennaservice}
+\includegraphics[width=5in]{images/rnaViennaServiceWindow.pdf}
+
+\caption{Secondary structure consensus calculations can be performed by enabling the
+VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+Structure} menu.}
+
+\end{center}
+\end{figure}
+
+\begin{figure}[htbp]
+\begin{center}
+\label{rnaviennaaltpairs}
+\includegraphics[width=5in]{images/rnaViennaAlternateProbs.pdf}
+
+\caption{VIENNA can calculate alternate RNA base pairing probabilities. These
+are shown in Jalview as tool-tips on the RNA secondary structure probability
+score.}
+
+\end{center}
+\end{figure}
+
+
+\exercise{Viewing RNA Structures}{
+\label{viewingrnaex}
+
+\exstep{Import RF00162 from Rfam (Full).}
+\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
+the secondary structure annotation provided by Rfam.}
+\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
+$\Rightarrow$ RNA Secondary Structure}.
+
+ Explore the difference between trimmed and untrimmed views for the
+ structure.
+}
+\exstep{Add and link a Jmol structure view
+for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
+structure along-side the consensus structure for the alignment by adding
+reference annotation from the 3D structure.
+
+{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
+Structure} preferences to obtain RNA secondary structure annotation from PDB
+files.}}
+
+\exstep{Perform a secondary structure prediction. Enable the VIENNA consensus
+calculation via the {\sl Web Services} menu. Compare this with the annotation
+line provided by Rfam.}
+
+\exstep{Edit the VIENNA calculation settings to show
+Base Pair probabilities.
+
+Explore how editing the alignment affects the consensus
+calculation.} }
+
- \end{document}
+\end{document}
git://source.jalview.org / jalview-manual.git / blobdiff