\title{Jalview 2.5: A manual and introductory tutorial }
\author{David Martin, James Procter, Andrew Waterhouse and Geoff Barton}
-\date{Manual version 1.2 9st June 2010}
+\date{Manual version 1.2.3 6th May 2011}
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}}\cleardoublepage}
{\Huge
-Jalview 2.5
+Jalview 2.7
}
\vspace{0.5in}
{\huge
\vspace{2in}
-Manual version 1.2
+Manual version 1.3.01
-8th June 2010
+6th December 2011
\end{center}
-\clearemptydoublepage
+\newpage
+
+% \clearemptydoublepage
-% ($Revision$) 1st September 2008.}
+% ($Revision$) 11th October 2010.}
+% TODO revise for 2.6
\pagenumbering{roman}
\setcounter{page}{1}
{\bf pfam}\footnote{\url{http://pfam.sanger.ac.uk}}.
-Jalview 2.5 was released in May 2010. The Jalview Desktop in this version
+Jalview 2.7 was released in September 2011. The Jalview Desktop in this version
provides access to sequence, alignment and protein structure databases, and
-alignment and analysis web services, and includes the Jmol\footnote{ Provided
-under the LGPL licence at \url{http://www.jmol.org}} protein structure viewer. It is
-also a Distributed Annotation System (DAS) client\footnote{with thanks to Andreas
-Prlic} which facilitates the retrieval and display of third party sequence
-annotation in association with sequences and any associated structure.
+includes the Jmol\footnote{ Provided under the LGPL licence at
+\url{http://www.jmol.org}} protein structure viewer. It includes a
+Distributed Annotation System (DAS) client\footnote{with thanks to Andreas Prlic} which facilitates the retrieval and display of third party sequence
+annotation in association with sequences and any associated structure. It also
+provides a graphical user interface for {\bf Ja}va {\bf B}ioinformatics
+{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS) which enable access to a
+range of multiple sequence alignment programs.
\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.
\begin{figure}[htbp]
\begin{center}
-\label{jvcapabilities}
\includegraphics[width=5.8in]{images/jvcapabilities.pdf}
\caption{{\bf Capabilities of the Jalview Desktop.} The Jalview Desktop Application provides a stable environment for the creation, editing and analysis of alignments and the generation of figures.}
+\label{jvcapabilities}
\end{center}
\end{figure}
Searle and Geoff Barton at the University of Oxford and then the European
Bioinformatics Institute. Development of Jalview 2 was made possible with
eScience funding from the BBSRC\footnote{Biotechnology and Biological Sciences
-Research Council grant {\sl "VAMSAS: Visualization and Analysis of Molecules,
+Research Council grant {\sl ``VAMSAS: Visualization and Analysis of Molecules,
Sequence Alignments and Structures"}, a joint project to enable interoperability
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.
+by an award from the BBSRC's Tools and Resources fund. In 2010 and 2011, 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.
+
+
%TODO describe future plans in history ? not a good idea.
% Jalview continues to be one of the worlds most popular\footnote{and in the authors opinion, the best.} sequence alignment and analysis tools.
\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
+{\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
+This paper supersedes the original Jalview publication:\newline {\sl ``The Jalview Java alignment
editor"} \newline Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey J. Barton (2004) \newline {\sl Bioinformatics} {\bf 20} 426-427.
\r\subsection{About this tutorial }
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}).
-Chapter \ref{analysisannotation} covers the additional visualization and analysis techniques that Jalview provides. This includes working with the embedded PDB structure viewer, building and viewing trees and PCA plots, and using trees for sequence conservation analysis. The use of the Jalview webservices for alignment and secondary structure prediction is described in Section \ref{jvwebservices}. Following this, Section \ref{featannot} details the creation and visualization of sequence and alignment annotation, and the retrieval of sequences and annotation from databases and DAS Servers. Finally, Section \ref{workingwithnuc} discusses specific features of use when working with nucleic acid sequences and protein coding regions.
+Chapter \ref{analysisannotation} covers the additional visualization and
+analysis techniques that Jalview provides. This includes working with the
+embedded Jmol molecular structure viewer, building and viewing trees and PCA
+plots, and using trees for sequence conservation analysis. An overview of
+the Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
+the alignment and secondary structure prediction services are described
+in detail in Sections \ref{msaservices} and \ref{protsspredservices}. Following
+this, Section \ref{featannot} details the creation and visualization of sequence
+and alignment annotation, and the retrieval of sequences and annotation from
+databases and DAS Servers. Finally, Section \ref{workingwithnuc} discusses
+specific features of use when working with nucleic acid sequences and protein
+coding regions.
%^Chapter \ref{jalviewadvanced} The third chapter covers the detail^ of Jalview and is aimed at the user who is
%already familiar with Jalview operation but wants to get more out of their
Jalview site. This behaviour can be changed in the Jalview Desktop preferences
dialog opened from the Desktop's {\sl Tools $\Rightarrow$ Preferences..} menu.
This alignment will look like the one in Figure \ref{startpage} (this is taken
-from the Jalview 2.4 manual).
+from Jalview version 2.7).
%[figure 3 ]
\begin{figure}[htbp]
\end{figure}
+\subsubsection{Jalview News RSS Feed}
+
+From time to time, important announcements are made available to users of the
+Jalview Destop {\sl via} the Jalview News reader. This window will open
+automatically when new news is available, and can also be accessed via the
+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
+when new articles are available from the Jalview Desktop's news channel.}
+\label{jalviewrssnews}
+\end{center}
+\end{figure}
+
+
\exercise{Starting Jalview}{
\label{start}
\exstep{Point your web browser at the \href{http://www.jalview.org}{Jalview web site} and start Jalview by clicking on the `Start with Java WebStart' 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 close Jalview and launch it
-again. The example alignment should not be loaded when Jalview starts up.}
-}
-
+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 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 to
+recover the example file's URL, followed by OK, to open the file. } }
\subsection{Getting Help}
\label{gettinghelp}
\subsection{The Find Dialog Box}
\label{searchfunction}
A further option for navigation is to use the {\sl Select $\Rightarrow$
-Find\ldots} function. This opens a dialog box into which can be entered regular expressions for searching sequences and sequence IDs, or sequence numbers. Hitting the [Find next] button will highlight the first (or next) occurence 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 comprehensive documentation for this function, and a quick guide to the regular expressions that can be used with it.
+Find\ldots} function. This opens a dialog box into which can be entered regular
+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 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
-\r\section{Loading your own sequences}\r\label{loadingseqs}\rJalview provides many ways to load your own sequences. %For this section of the tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.\r\r\subsection{Drag and Drop}\r In some operating systems (Mac OS X, Windows XP) 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.\rIf you drop an alignment file onto an open alignment window it will be appended to that alignment.\r% (Figure \ref{drag})
+\r\section{Loading your own sequences}\r\label{loadingseqs}\rJalview provides many ways to load your own sequences. %For this section of the tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.\r\r\subsection{Drag and Drop}\r In most operating systems you can just drag a file icon from a file browser\r window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended\rto that alignment. Drag and drop also works when loading data from a URL -\rsimply drag the link or url from the address panel of your browser on to an\ralignment or the Jalview desktop background and Jalview will load data from the\rURL directly.\r% (Figure \ref{drag})
% %[fig 5]\r% \begin{figure}[htbp]\r% \begin{center}\r% \includegraphics[width=2in]{images/drag2.pdf}\r% \includegraphics[width=2in]{images/drag3.pdf}\r% \caption{{\bf An alignment can be opened by dragging the file onto the Jalview window. }}\r% \label{drag}\r% \end{center}\r% \end{figure}\r% \r% %\includegraphics[width=2in]{images/drag1.pdf}
\r\subsection{From a File}\r Jalview can read sequence alignments from a sequence alignment file. This is a text file, not a word processor document. For entering sequences from a wordprocessor document see Cut and Paste (Section \ref{cutpaste}) below. Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu (Figure \ref{loadfile}). You will then get a file selection window where you can choose the file to open. Remember to select the appropriate file type. Jalview can automatically identify some sequence file formats.\r\r%[fig 6]\r\begin{figure}[htbp]
\end{center}
\end{figure}
\r\subsection{Cut and Paste}
-\label{cutpaste}\rDocuments such as those produced by Microsoft Word cannot be readily understood\rby Jalview. The way to read sequences from these documents is to select the\rdata from the document and copy it to the clipboard. There are two ways to\rdo this. One is to right-click on the desktop background, and select the\r'Paste to new alignment' option in the menu that appears. The other is to select\r{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the\rmain menu, and paste the sequences into the textbox window that will appear\r(Figure \ref{loadtext}). In both cases, presuming that they are in the right\rformat, Jalview will happily read them into a new alignment window.\r%[fig 8]
+\label{cutpaste}\rDocuments such as those produced by Microsoft Word cannot be readily understood\rby Jalview. The way to read sequences from these documents is to select the\rdata from the document and copy it to the clipboard. There are two ways to\rdo this. One is to right-click on the desktop background, and select the\r`Paste to new alignment' option in the menu that appears. The other is to select\r{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the\rmain menu, and paste the sequences into the textbox window that will appear\r(Figure \ref{loadtext}). In both cases, presuming that they are in the right\rformat, Jalview will happily read them into a new alignment window.\r%[fig 8]
\begin{figure}[htbp]
\begin{center}
\exstep{Start Jalview then close all windows by selecting {\sl Window $\Rightarrow$ Close All} from the main menu}
\exstep{Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box. Click {\sl OK} and the alignment should load.
}
-\exstep{Close all windows using the {\sl Window $\Rightarrow$ Close All} main menu option. Point your web browser to \textsf{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 browsing to the appropriate location. Click OK and load the alignment
-}
-\exstep{
-Drag the alignment.fa file from the desktop onto the Jalview window. The alignment should open. Try dragging onto an empty Jalview and onto an existing alignment and observe the results.
-}
-\exstep{
-Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the {\sl PFAM (seed)} database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load.
-}
-\exstep{Open the URL \textsf{http://www.jalview.org/tutorial/alignment.fa} in a web browser. Select and copy the entire text to the clipboard (usually via the browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} . Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$ Paste} text box menu option. Click {\sl Close} and the alignment will be loaded.
-}
-}
+\exstep{Close all windows using the {\sl Window $\Rightarrow$ Close All} main
+menu option. Point your web browser at the same \href{http://www.jalview.org/tutorial/alignment.fa}{URL} and save the file to
+your desktop. Open this file in Jalview by selecting {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu and browsing to the appropriate location. Click OK and load the alignment }
+\exstep{Drag the alignment.fa file from the desktop onto the Jalview window. The
+alignment should open. Try dragging onto an empty Jalview and onto an existing
+alignment and observe the results. You can also try dragging the
+\href{http://www.jalview.org/tutorial/alignment.fa}{URL} directly onto Jalview.
+}
+\exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the {\sl PFAM (seed)} database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. }
+\exstep{Open the \href{http://www.jalview.org/tutorial/alignment.fa}{URL} in a
+web browser. Select and copy the entire text to the clipboard (usually via the
+browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running
+and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} .
+Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
+Paste} text box menu option. Click {\sl New Window} and the alignment will be
+loaded. } }
\subsection{Memory Limits}
\label{memorylimits}
\exercise{Saving Alignments}{
\label{save}
-\exstep{Start Jalview, close all windows and load the ferredoxin alignment from pFam (accession number PF03460 (see Exercise \ref{load}).
-}
+\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 browsing to it with your web browser or by closing all windows and opening it with Jalview.
}
\exstep{ Repeat the previous step trying different file formats.}
\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}. You can select and copy this alignment to the clipboard using the textbox menu options {\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}. The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
}
-\exstep{Ensure at least one alignment window is shown in Jalview. Open the overview window and scroll to any part of the alignment. Select {\sl File $\Rightarrow$ Save Project} from the main menu and save in a suitable place. Close all windows and then load the project via the {\sl File $\Rightarrow$ Save Project} menu option. Note how all the windows and positions are exactly as they were when they were saved.
-}
-}
+\exstep{Ensure at least one alignment window is shown in Jalview. Open the
+overview window and scroll to any part of the alignment. Select {\sl File
+$\Rightarrow$ Save Project} from the main menu and save in a suitable place.
+Close all windows and then load the project via the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } }
\r\r\section{Selecting and editing sequences}
\label{selectingandediting} \rJalview makes extensive use of selections - most of the commands available from
its menus operate on the currently selected region of the alignment, either to
\r\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 $\Rightarrow$ As New Alignment} alignment window menu options.
+A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ New Alignment} alignment window menu options.
To clear (unselect) the selection press the [ESC] (escape) key.
\subsubsection{Making selections in Cursor mode}
-To define a selection in cursor mode, navigate to the top left corner of the proposed selection. Pressing the [Q] key marks this as the corner. A red outline appears around the cursor (Figure \ref{cselect})
+To define a selection in cursor mode (which is enabled by pressing [F2]),
+navigate to the top left corner of the proposed selection (using keystroke
+commands, the arrow keys or the mouse). Pressing the [Q] key marks this as the
+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.
visible, and then invert the selection.\footnote{It is also possible to hide
everything but the selected region using the {\sl View $\Rightarrow$ Hide
$\Rightarrow$ All but selected region } menu entry.}
-\r\r\subsection{Creating groups}\rSelections are lost as soon as a different region is selected. Groups can be created which are labeled regions of the alignment. To create a group, first select the region which is to comprise the group. Then click the right mouse button on the selection to bring up a context menu. Select {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group} then enter a name for the group in the dialogue box which appears.
+\r\r\subsection{Creating groups}\rSelections are lost as soon as a different region is selected. Groups can be
+created which are labeled regions of the alignment. To create a group, first
+select the region which is to comprise the group. Then click the right mouse
+button on the selection to bring up a context menu. Select {\sl Selection
+$\Rightarrow$ Group $\Rightarrow$ Edit name and description of
+current group}\footnote{In earlier versions of Jalview, this entry was variously
+`Group', `Edit Group Name', or `JGroupXXXXX' (Where XXXXX was some serial
+number).} then enter a name for the group in the dialogue box which appears.
\begin{figure}
\begin{center}
\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. }
+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.}
}
\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 shiting 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.
+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.
\subsubsection{Introducing gaps in a single sequence}
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).
+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 -
+which, for example, allows you to easily reposition misaligned subfamilies
+within a larger alignment.
\subsubsection{Undoing edits}
-Jalview supports the undoing of edits via the {\sl Edit $\Rightarrow$ Undo Edit} alignment window menu option. Each editing action is stored and can be reversed in sequence. Colouring of the alignment is not reversible via the {\sl Undo} option.
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit1.pdf}
-\includegraphics[width=3in]{images/edit2.pdf}
-\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
-selected sequence is dragged to the right with [SHIFT] pressed.}
-\label{gapseq}
-\end{center}
-\end{figure}
+Jalview supports the undoing of edits via the {\sl Edit $\Rightarrow$ Undo Edit}
+alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
+with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
+{\sl Undo} function only works for edits to the alignment or sequence ordering.
+Colouring of the alignment, showing and hiding of sequences or modification of
+annotation cannot be undone.
-\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}
% % better idea to introduce hiding sequences, and use the invert selection, hide
% others, to simplify manual alignment construction
\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
+ available at
+ \href{http://www.jalview.org/examples/exampleFile.jar}{http://www.jalview.org/examples/exampleFile.jar}.
+}
+ \item{Remember to use [CTRL]+Z to undo an edit, or the {\tr File $\Rightarrow$
+ Reload } function to revert the alignment back to the original version if you
+ want to start again.}
+ \item{ If you are using OSX, and a key combination - such as [CTRL]+A - does
+ not work, then try pressing the [CMD] key instead of [CTRL].
+ }
+\item{}
+
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
ferredoxin alignment from PF03460.
-
- You are going to manually reconstruct the alignment that jalview loads by
- default. Remember to use [CTRL]+Z to undo an edit, or the {\tr File $\LeftArrow$
- Reload } function to revert the alignment back to the original version if you
- want to start again.
- }
+}
\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 {\tr Hide
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
O80429\_MAIZE (Hint: press [CTRL]-I to invert the sequence selection and then
-deleset FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they
+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
the same way.}
\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
-insert two additional gaps after the gap at column 47: hold [SHIFT] and click and
-drag on the G and move it two columns to the right.}
+insert two additional gaps after the gap at column 47: First press [Escape] to
+clear the selection, then hold [SHIFT] and click and drag on the G and move it
+two columns to the right.}
\exstep{ Now complete the
alignment of FER1\_SPIOL with a {\bf locked edit} by pressing [ESC] and select
\exstep{ Hold [SHIFT] and drag the I at column 39 of FER1\_MAIZE 2 columns to the
right. Remove the gap at FER1\_MAIZE column 49 by [SHIFT]+click and drag left by
-one column. Insert three gaps in FER1\_MAIZE at column 47 by holding [SHIFT] and
-click and drag the S in FER1\_MAIZE to the right by three columns. Finally,
+one column. Press [Escape] to clear the selection, and then insert three gaps in
+FER1\_MAIZE at column 47 by holding [SHIFT] and click and drag the S in FER1\_MAIZE to the right by three columns. Finally,
remove the gap in O80429\_MAIZE at column 56 using [SHIFT]-drag to the left on
42R.}
\exstep{ Use the
-{\sl Edit $\Rightarrow$ Undo Edit} and {\sl Edit $\Rightarrow$ Redo Edit} menu option to step backwards and replay the
-edits you have made}
-}
+{\sl Edit $\Rightarrow$ Undo Edit} and {\sl Edit $\Rightarrow$ Redo Edit} menu
+option, or their keyboard shortcuts ([CTRL]+Z and [CTRL]+Y) to step backwards
+and replay the edits you have made} }
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit1.pdf}
+\includegraphics[width=3in]{images/edit2.pdf}
+\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
+selected sequence is dragged to the right with [SHIFT] pressed.}
+\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 removed in cursor mode by pressing [BACKSPACE]. The gap under the cursor will be removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps will be deleted up to the number specified. To delete gaps from all sequences of a group, use [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down together).
\exercise{Keyboard edits}{
-\exstep{Load the sequence alignment at \textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the edited alignment from exercise \ref{mousealedit}. If you continue from the previous exercise, then first right click on the sequence ID panel and select {\tr Reveal All}.
+\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.}
+
+\exstep{Load the
+sequence alignment at \textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the edited alignment from exercise \ref{mousealedit}. If you continue from the previous exercise, then first right click on the sequence ID panel and select {\tr Reveal All}.
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 [CTRL] and press the space bar.}
\end{figure}
\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} brings up a selection box (the {\sl Conservation Threshold dialog box}) allowing the alignment colouring to be modified. Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}).
+For many colour schemes, the intensity of the colour in a column can be scaled
+by the degree of amino acid property conservation. Selecting {\sl Colour
+$\Rightarrow$ By Conservation} enables this mode, and {\sl Modify
+conservation threshold} brings up a selection box (the {\sl Conservation
+Threshold dialog box}) allowing the alignment colouring to be modified.
+Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}).
\begin{figure}[htbp]
\begin{center}
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).
\subsection{Colouring by Annotation}
+\label{colourbyannotation}
\parbox[c]{3in}{
Any of the quantitative annotations shown on an alignment can be used to
threshold or shade the whole alignment\footnote{Please remember to turn off
Sequence Feature display to see the shading}. The {\sl Colour $\Rightarrow$ By
Annotation} options opens a dialog which allows you to select which annotation
to use, the minimum and maximum shading colours or whether the original
-colouring should be thresholded (the `Use original colours' option).
-}\parbox[c]{3in}{
+colouring should be thresholded (the `Use original colours' option).
+
+Default settings for the minimum and maximum colours can be set in the Jalview
+Desktop's preferences. }\parbox[c]{3in}{
\centerline{\includegraphics[width=2.5in]{images/col_byannot.pdf}}}
\subsection{Colour schemes}
\subsubsection{Fonts}
-\parbox[c]{4in}{The text appearance in a view can be modified via the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignnment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
+\parbox[c]{4in}{The text appearance in a view can be modified 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}
\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 protein sequences in the alignment. The Java based molecular viewing program Jmol\footnote{See the Jmol homepage \url{http://www.jmol.org} for more information.} has been incorporated\footnote{Earlier versions of Jalview included MCView - a simple main chain structure viewer. Structures are visualized as an alpha carbon trace and can be viewed, rotated and coloured in a structure viewer and the results interpreted on a sequence alignment.} which enables sophisticated molecular visualizations to be prepared and investigated alongside an analysis of associated sequences.
-PDB format files can be imported directly or structures can be retrieved from the the Macromolecular Structure Database (MSD) using the Sequence Fetcher (see \ref{fetchseq}).
+PDB format files can be imported directly or structures can be retrieved from
+the European Protein Databank (PDBe) using the Sequence Fetcher (see
+\ref{fetchseq}).
\subsection{Automatic association of PDB structures with sequences}
Jalview can automatically determine which structures are associated with a
-sequence if that sequence has an ID from a public database that contains
-cross-references to the PDB, such as Uniprot. Right-click on any sequence ID and
-select {\sl $<$Sequence ID$>$ $\Rightarrow$ Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the
-context menu (where {\sl $<$Sequence ID$>$} is the ID of the sequence on which
+sequence in a number of ways.
+\subsubsection{Discovery of PDB ids from sequence database cross-references}
+if a sequence has an ID from a public database that contains cross-references to
+the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl $<$Sequence ID$>$ $\Rightarrow$ Structure $\Rightarrow$
+Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (where {\sl $<$Sequence ID$>$} is the ID of the sequence on which
you clicked) (Figure \ref{auto}). Jalview will attempt to associate the
sequence with a Uniprot sequence and from there discover any associated PDB
structures. This takes a few seconds and applies to all sequences in the
\end{center}
\end{figure}
+\subsubsection{Drag-and-drop association of PDB files with sequences by filename
+match}
+\label{multipdbfileassoc}
+If one or more PDB files are dragged from a file browser onto an alignment
+window, Jalview will search the alignment for sequences with IDs that
+matches any of the files dropped onto the alignment. If it discovers matches, a
+dialog like the one in Figure \ref{multipdbfileassocfig} is shown, giving the
+option of creating associations for the matches.
+
+If no associations are made, then sequences extracted
+from the structure will be simply appended to the alignment. However, if only
+some of the files are associated, jalview will raise another dialog box giving
+you the option to add any remaining sequences the structure files not present in
+the alignment. This allows you to easily decorate sequences in a newly imported
+alignment with any corresponding structures you've collected in a directory
+accessible from your computer.\footnote{We plan to extend this facility in
+future so Jalview will automatically search for PDB files matching your
+sequence within a local directory. Check out
+\href{http://issues.jalview.org/browse/JAL-801}{Jalview issue 801}}
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[]{images/pdbdragdropassoc.pdf}
+
+\caption{{\bf Associating PDB files with sequences by drag-and-drop.} Dragging
+PDB files to an alignment of sequences with names matching the dragged
+files names (A), results in a dialog box (B) that gives the option to associate each file with any sequences with matching IDs. }
+\label{multipdbfileassocfig}
+\end{center}
+\end{figure}
+
+
\subsection{Viewing Protein Structures}
-The structure viewer can be launched through the sequence ID context menu.
-Select {\sl Structure $\Rightarrow$ View PDB entry $\Rightarrow$ $<$PDB
-ID$>$}. The structure will be downloaded or loaded from the local file system,
-and shown as a ribbon diagram coloured according to the associated sequence in
-the current alignment view (Figure \ref{structure} (right)). The structure can
-be rotated by clicking and dragging in the structure window. The structure can
-be zoomed using the mouse scroll wheel (if available). Moving the mouse cursor
-over a sequence to which the structure is linked in the alignment panel
-highlights the respective residue's sidechain atoms. The sidechain highlight
-may be obscured by other parts of the molecule. Similarly, moving the cursor
-over the structure shows a tooltip and highlights the corresponding residue in
-the alignment. Often, the position highlighted may not be in the visible
-portion of the current alignment view. If the alignment window's {\sl View
-$\Rightarrow$ Automatic Scrolling } option is not selected, then you may have
-to manually move the alignment scroll bars to see the highlighted region.
+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
+{\sl Structure $\Rightarrow$ View Structure $\Rightarrow$ $<$PDB ID$>$}. The
+second way is most useful if you want to view all structural data available for
+a set of sequences in an alignment. If any of the {\bold currently selected}
+sequences have structures associated, the {\sl Structure } submenu of the
+sequence ID popup menu will include an option to {\sl View {\bold N}
+structures}. Selecting this option will open a new structure view containing
+the associated structures superposed according to the alignment.
+
+In both cases, each structure to be displayed will be downloaded or loaded from
+the local file system, and shown as a ribbon diagram coloured according to the
+associated sequence in the current alignment view (Figure \ref{structure}
+(right)). The structure can be rotated by clicking and dragging in the structure
+window. The structure can be zoomed using the mouse scroll wheel (if available).
+Moving the mouse cursor over a sequence to which the structure is linked in the
+alignment panel highlights the respective residue's sidechain atoms. The
+sidechain highlight may be obscured by other parts of the molecule. Similarly,
+moving the cursor over the structure shows a tooltip and highlights the
+corresponding residue in the alignment. Often, the position highlighted may not
+be in the visible portion of the current alignment view. If the alignment
+window's {\sl View $\Rightarrow$ Automatic Scrolling } option is not selected,
+then you may have to manually move the alignment scroll bars to see the
+highlighted region.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{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 {\sl Colours $\Rightarrow$ Background Colour\ldots} option.
+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
+{\sl Colours $\Rightarrow$ Background Colour\ldots} option.
-By default, the structure will be coloured in the same way as the sequence in the associated alignment view. The structure can be coloured independently of the sequence by selecting an appropriate colour scheme from the {\sl Colours} menu. It can be coloured according to the alignment using the {\sl Colours $\Rightarrow$ By Sequence } option. The image in the structure viewer can be output to EPS or PNG format via the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots} submenu. The mapping between the structure and the 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.
+By default, the structure will be coloured in the same way as the
+associated sequence(s) in the alignment view from which it was launched. The
+structure can be coloured independently of the sequence by selecting an
+appropriate colour scheme from the {\sl Colours} menu. It can be coloured
+according to the alignment using the {\sl Colours $\Rightarrow$ By Sequence } option. The image in the structure viewer can be
+output to EPS or PNG format via the {\sl File $\Rightarrow$ Save As
+$\Rightarrow$ \ldots} submenu. The mapping between the structure and the
+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 }
the view. It also has its own ``Rasmol\footnote{see
http://www.rasmol.org}-like'' scripting language, which is described elsewhere\footnote{Jmol Wiki: \url{http://wiki.jmol.org/index.php/Scripting}
-Jmol Scripting reference: \url{http://www.stolaf.edu/academics/chemapps/jmol/docs/}}. Jalview utilises the scripting language to interact with Jmol and to store the state of a Jmol visualization within Jalview archives, in addition to the PDB data file originally loaded or retrieved by Jalview. To access the Jmol scripting environment directly, use the {\sl Jmol $\Rightarrow$ Console} menu option.
-
-
-\exercise{Viewing Structures}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Associate Structure with Sequence $\Rightarrow$ Discover PDB ids}. Jalview will now attempt to find PDB structures for the sequences in the alignment.
-}
-\exstep{
-Right-click on the sequence ID for {\sl FER1\_SPIOL}. Select { \sl FER1\_SPIOL $\Rightarrow$ View PDB Entry: 1A70} A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel.
-}
-\exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence.
-}
-\exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press {\sl OK} to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with your web browser.
-}
+Jmol Scripting reference:
+\url{http://www.stolaf.edu/academics/chemapps/jmol/docs/}}. Jalview utilises the
+scripting language to interact with Jmol and to store the state of a Jmol visualization within Jalview archives, in addition to the PDB data file originally loaded or retrieved by Jalview. To access the Jmol scripting environment directly, use the {\sl Jmol $\Rightarrow$ Console} menu option.
+
+If you would prefer to use Jmol to manage structure colours, then select the
+{\sl Colours $\Rightarrow$ Colour with Jmol} option. This will disable any
+automatic application of colour schemes when new structure data is added, or
+when associated alignment views are modified.
+
+
+\exercise{Viewing Structures}{\label{viewingstructex}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the
+sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up
+the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
+Associate Structure with Sequence $\Rightarrow$ Discover
+PDB ids}. Jalview will now attempt to find PDB structures for the sequences in
+the alignment. } \exstep{ Right-click on the sequence ID for {\sl FER1\_SPIOL}.
+Select { \sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$ View Structure
+$\Rightarrow$ 1A70} A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel. } \exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. } \exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press {\sl OK} to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with your web browser. }
\exstep{Select {\sl File $\Rightarrow$ View Mapping} from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.}
\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file. Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
Verify that the Jmol display is as it was when you just saved the file.}
}
+\subsection{Superimposing structures}
+\label{superposestructs}
+Many comparative biomolecular analysis investigations aim to determine if the
+biochemical properties of a given molecule are signficantly different to its
+homologues. When structure data is available, comparing the shapes of molecules
+by superimposing them enables substructure that may impart different behaviour
+to be quickly identified. The identification of optimal 3D superpositions
+involves aligning 3D data rather than sequence symbols, but the result can
+still be represented as a sequence alignment, where columns indicate positions
+in each molecule that should be superposed to recreate the optimal 3D alignment.
+
+Jalview can employ Jmol's 3D fitting routines\footnote{See
+\href{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2#compare}{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}
+for more information.} to recreate 3D structure superpositions based on the
+correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view happens automatically if a
+structure is added to an existing Jmol display using the {\sl Structure
+$\Rightarrow$ View PDB Structure $\Rightarrow$ ..}. A new Jmol view containing
+superposed structures can also be created using the {\sl Structure
+$\Rightarrow$ View all {\bf N} PDB Structures} option (when {\bf {\sl N}}
+$>$ 1) if the current selection contains two or more sequences with associated
+structures.
+
+\subsubsection{Obtaining the RMSD for a superposition}
+Figure \ref{mstrucsuperposition} shows a superposition created during the course
+of Exercise \ref{superpositionex}. The parts of each molecule used to construct
+the superposition are rendered using the cartoon style, with other parts of
+the molecule drawn in wireframe. The Jmol console, which has been opened after
+the superposition was performed, shows the RMSD report for the superposition.
+Full information about the superposition is also output to the Jalview console,
+including the precise atom pairs used to superpose structures.
+
+\subsubsection{Choosing which part of the alignment is used for structural
+superposition}
+Jalview uses the visible part of each alignment view to define which parts of
+each molecule are to be corresponded. Hiding a column in a view used for
+superposition will remove that correspondence from the set, allowing
+the selection of specific parts of the alignment to be used for
+superposition. Only columns that define a complete set of correspondences for
+all structures will be used for structural superposition, and as a consequence,
+the RMSD values generated for each pair of structures superimposed can be
+directly compared.
+
+In order to recompute a superposition after changing a view or editing the
+alignment, select the {\sl Jmol $\Rightarrow$ Align } menu option. The {\sl
+Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
+associated alignments and views are to be used to create the set of
+correspondences. This menu is useful when composing complex superpositions
+involving multi-domain and multi-chain complexes, when correspondences may be
+defined by more than one alignment.
+
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
+\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
+left was used by jalview to superpose structures associated with the
+FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
+used for superposition are rendered as a cartoon, the remainder rendered in
+wireframe. The RMSD between corresponding positions in the structures before and
+after the superposition is shown in the Jmol console. }
+\label{mstrucsuperposition}
+\end{center}
+\end{figure}
+
+\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
+IDs associated with the FER1\_MAIZE sequence.}
+\exstep{Once discovery has completed, use the {\sl
+View PDB Structure} submenu to view the PDB file associated with FER1\_MAIZE.
+Jalview will give you the option of aligning the structure to the one already
+open. To superimpose the structure associated with FER1\_MAIZE with the one
+associated with FER1\_SPIOL, press the {\bf Yes} button.
+
+{\sl The Jmol view will update to show both structures, and one will be
+moved on to the other.}}
+\exstep{Create a new view on the alignment, and hide all but columns 121
+through to 132.}
+\exstep{Use the {\sl Jmol} submenu to
+recompute the superposition using just columns 121-132 of the alignment.
+
+{\sl Note how the molecules shift position when superposed using a short part of
+the two structures.}}
+\exstep{Compare the initial and final RMSDs for superimposing molecules with
+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
+opened will be the one used to colour structure data. If alignments involving
+sequences associated with structure data shown in a Jmol have multiple views, Jalview gives you full control
+over which alignment, or alignment view, is used to colour the structure
+display. Sequence-structure colouring associations are
+changed {\sl via} the {\sl View $\Rightarrow$ Colour by} menu, which lists all
+views associated with data shown in the embedded Jmol view. A tick is shown beside
+views currently used as colouring source, and moving the
+mouse over each view will bring it to the front of the alignment display,
+allowing you to browse available colour sources prior to selecting one. If the
+{\sl Select many views} option is selected, then multiple views can be selected as sources for colouring the
+structure data. {\sl Invert selection} and {\sl Select all} options are also provided to quickly change between multi-view selections.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/mviewstructurecol.pdf}
+\caption{{\bf Choosing a different view for colouring a structure display}
+Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control
+of which alignment view is used to colour structures when the {\sl Colour
+$\Rightarrow$ Colour by sequence} option is selected.}
+\label{mviewstructurecol}
+\end{center}
+\end{figure}
+
+\subsubsection{Colouring complexes}
+
+The ability to control which multiple alignment or view is used to colour
+structural data is essential when working with data relating to
+multidomain biomolecules and complexes.
+
+In these situations, each chain identified in the structure may have a different
+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
+DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Jikui Song, Olga Rechkoblit, Timothy H. Bestor, and Dinshaw J. Patel.
+{\sl Science} {\bf 331} 1036-1040
+\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[]{images/mchainstructureview.pdf}
+\caption{{\bf The biological assembly of Mouse DNA Methyltransferase-1 coloured
+by Pfam alignments for its major domains} Alignments for each domain within the
+Uniprot sequence DNMT1\_MOUSE have been used to visualise sequence conservation
+in each component of this protein-DNA complex. Instructions for recreating this figure are given in exercise \ref{dnmtcomplexex}. }
+\label{mviewalcomplex}
+\end{center}
+\end{figure}
+
+\exercise{Colouring a protein complex to explore domain-domain interfaces}{\label{dnmtcomplexex}
+
+\exstep{Download the PDB file at
+\textsf{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}}.}
+\exstep{Retrieve the following
+{\bf full} PFAM alignments: PF02008, PF00145, PF01426. These will each be retrieved into their own alignment window.}
+\exstep{Drag the structure you downloaded in
+step 1 onto one of the alignments to associate it with the mouse sequence in
+that Pfam domain family.}
+\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
+ID popup menu's structure submenu to view the DNMT1\_MOUSE structure for the associated mouse sequence. Check the contents of
+the {\sl View $\Rightarrow$ Colour by ..} submenu to see what alignments can be used to
+colour the sequence.}
+\exstep{Repeat the previous two steps for each of
+the other alignments. In each case, when performing the `View DNMT1\_MOUSE.pdb'
+step, Jalview will ask you if you wish to create a new Jmol view. You should
+respond `No', ensuring that each sequence fragment is associated with the same Jmol view.}
+\exstep{Pick a different colourscheme for each alignment, and use the {\sl
+Colour by ..} submenu to ensure they are all used to colour the complex shown
+in the Jmol window.}
+\exstep{The final step needed to reproduce the shading in Figure
+\ref{mviewalcomplex} is to use the {\sl Colour $\Rightarrow$ By
+Annotation } option in each alignment window to shade the alignment by the
+{\bf Conservation} annotation row. This function was described in section
+\ref{colourbyannotation}.
+
+{\sl Note: Choose a different shading scheme for each
+alignment so that the regions of strong physicochemical conservation are highlighted. This
+kind of shading will reveal conserved regions of interaction between domains
+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).} }
+
\section{Analysis of alignments}
\label{alignanalysis}
Jalview provides support for sequence analysis in two ways. A number of analytical methods are `built-in' and run inside Jalview itself and are mostly accessed from the {\sl Calculate} alignment window menu. Computationally intensive analyses are run outside Jalview via web services - these are typically accessed via the {\sl Web Services} menu, and described in Section \ref{jvwebservices}. In this section, we describe the built-in analysis capabilities common to both the Jalview Desktop and the JalviewLite applet.
Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$ Show Labels} menu option, and the plot background colour changed via the {\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical representation of the PCA plot can be exported as an EPS or PNG image via the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
\exercise{Principle Component Analysis}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/examples/exampleFile.jar} and select {\sl Edit $\Rightarrow$ Undefine Groups}.
-}
-\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/examples/exampleFile.jar} and select {\sl Select
+$\Rightarrow$ Undefine Groups}. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
\exstep{
Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups, each of a different colour. Note how the colour of the sequence ID label matches both the colour of the partitioned tree and the points in the PCA plot.
}
Jalview can calculate and display trees, providing interactive tree-based grouping of sequences though a tree viewer. All trees are calculated via the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu. Trees can be calculated from distance matrices determined from \% identity or aggregate BLOSUM 62 score using either average distance (UPGMA) or Neighbour joining algorithms. The input data for a tree calculation is either the visible portions of the current selection, or the whole alignment if no selection is present.
On calculating a tree, a new window opens (Figure \ref{trees1}) which contains
-the tree. Various display options can be found in the tree window {\sl View}
-menu, and export options in the {\sl File $\Rightarrow$ Save As} submenu.
-Newick format is a standard file format for trees which allows them to be
-exported to other programs. Jalview can also read in external trees in Newick
-format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf
-names on imported trees will be matched to the associated alignment - unmatched
+the tree. Various display settings can be found in the tree window {\sl View}
+menu, including font, scaling and label display options, and the {\sl File
+$\Rightarrow$ Save As} submenu contains options for image and Newick file
+export. Newick format is a standard file format for trees which allows them to
+be exported to other programs. Jalview can also read in external trees in Newick format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf names on imported trees will be matched to the associated alignment - unmatched
leaves will still be displayed, and can be highlighted using the {\sl View
$\Rightarrow$ Show Unlinked Leaves} menu option.
can help when working with larger alignments.
\exercise{Tree Based Conservation Analysis}{
+\label{consanalyexerc}
\exstep{Load the PF03460 Seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the sort submenu to order alignment using the calculated tree.}
\exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
\end{figure}
\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{treeconsanaly})}
+\exstep{Re-use or recreate the alignment and tree which you worked with in the
+tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% similar under this alignment.}
\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Show Linked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
\exstep{Use the [Undo] button on the dialog to recover the sequences. Note that the * symbols disappear from the tree display.}
consensus row will be shown, but for amino acid sequences,
alignment quality (based on BLOSUM62) and physicochemical conservation will
also be shown. Conservation is calculated according to Livingstone and
-Barton\footnote{{\sl "Protein Sequence Alignments: A Strategy for the Hierarchical Analysis of Residue Conservation."
+Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the Hierarchical Analysis of Residue Conservation."
} Livingstone C.D. and Barton G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
Consensus is the modal residue (or {\tt +} where there is an equal top
residue). The inclusion of gaps in the consensus calculation can be toggled by
The consensus annotation row that is shown below the alignment can be overlaid
with a sequence logo that reflects the symbol distribution at each column of
-the alignment. Right click on the Consensus annotation row and select the 'Show
+the alignment. Right click on the Consensus annotation row and select the `Show
Logo' option to display the Consensus profile for the group or alignment.
Sequence logos can be enabled by default for all new alignments {\sl via} the
Visual tab in the Jalview desktop's preferences dialog box.
\exercise{Group conservation analysis}{
-\exstep{Re-use or recreate the alignment and tree which you worked with in the tree based conservation analysis exercise (exercise \ref{treeconsanaly})}
-\exstep{Create a new view, and ensure the annotation panel is displayed, and
+\exstep{Re-use or recreate the alignment and tree which you worked with in the
+tree based conservation analysis exercise (exercise \ref{consanalyexerc})} \exstep{Create a new view, and ensure the annotation panel is displayed, and
enable the display of {\sl Group Consensus}, and the display of sequence
logos to make it easier to see the different residue populations within each group.}
\exstep{Select a column exhibiting about 50\% conservation that lies within the
services are `one-way', {\sl i.e.} data is either sent to the webservice or
retrieved from it by Jalview. The desktop application can also interact
with `two-way' remote analysis services in order to offload computationally
-intensive tasks to High Performance Computing facilities.}
+intensive tasks to High Performance Computing facilities. Most of these two-way
+services are provided by {\bf Ja}va {\bf B}ioinformatics {\bf A}nalysis {\bf
+W}eb {\bf S}ervice (JABAWS) servers\footnote{See
+http://www.compbio.dundee.ac.uk/jabaws for more information and to download
+your own server.}, which provides an easily installable system for performing
+a range of bioinformatics analysis tasks. }
\parbox[c]{1.75in}{\includegraphics[width=1.65in]{images/wsmenu.pdf}}
\subsection{One way web services}
presented in the submenus, then try to select a smaller number of sequences to
submit.
-\subsection{Remote Analysis Services}
+\subsection{Remote Analysis Web Services}
Remote analysis services enable Jalview to use external computational
-facilities. There are curently two types of service - multiple sequence
-alignment and protein secondary structure prediction. In both cases, Jalview
-will construct a job based on the alignment or currently selected sequences, ask
-the remote server to run the job, monitor status of the job and, finally,
-retrieve the results of the job and display them. The Jalview user is kept
-informed of the progress of the job through a status window.
+facilities. There are curently three types of service - multiple sequence
+alignment, protein secondary structure prediction, and alignment analysis.
+Many of these are provided by JABA servers, which are described at the end of
+this section. In all cases, Jalview will construct a job based on the alignment
+or currently selected sequences, ask the remote server to run the job, monitor
+status of the job and, finally, retrieve the results of the job and display
+them. The Jalview user is kept informed of the progress of the job through a
+status window.
Currently, web service jobs and their status windows are not stored in Jalview
Project Files\footnote{This may be rectified in future versions.}, so it is
successfully use Web Services from Jalview, since it periodically checks the
progress of running jobs.
-\subsection{Multiple Sequence Alignment}
-Sequences can be aligned using any of three algorithms: ClustalW\footnote{{\sl "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."} Thompson JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic Acids Research} {\bf 22}, 4673-80}, Muscle\footnote{{\sl "MUSCLE: a multiple sequence alignment method with reduced time and space complexity"} Edgar, R.C. (2004) {\sl BMC Bioinformatics} {\bf 5}, 113} or MAFFT\footnote{{\sl "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform"} Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) {\sl Nucleic Acids Research} {\bf 30}, 3059-3066. and {\sl "MAFFT version 5: improvement in accuracy of multiple sequence alignment"} Katoh, K., Kuma, K., Toh, H. and Miyata, T. (2005) {\sl Nucleic Acids Research} {\bf 33}, 511-518.} Of these, ClustalW is the slowest but is historically the most widely used. Muscle is fast and probably the most accurate for smaller alignments and MAFFT is probably the best for large alignments.
+\subsection{JABA Web Services for sequence alignment and analysis}
+JABA stands for ÔJAva Bioinformatics AnalysisÕ, which is a system developed by
+Peter Troshin and Geoff Barton at the University of Dundee for running
+computationally intensive bioinformatics analysis programs. A JABA installation
+typically provides a range of JABA web services (JABAWS) for use by other
+programs, like Jalview.
+
+Exercises in the remainder of this section will demonstrate the simplest way of
+installing JABA on your computer, and configuring Jalview so it can access the JABA services. If you
+need any further help or more information about the services, please go to the
+\href{http://www.compbio.dundee.ac.uk/jabaws}{JABAWS home page}.
+%% \subsubsection{Aims}
+%% \begin{list}{$\bullet$}{}
+%% \item Gain experience using the different alignment services provided by
+% JABA
+%%\item Learn about the way that Jalview stores user presets for JABA services
+%%\item Learn how to install JABA services and configure Jalview to access them
+%%\end{list}
+
+\subsection{Changing the Web Services menu layout}
+\label{changewsmenulayout}
+If you are working with a lot of different JABA services, you may wish to
+change the way Jalview lays out the web services menu. You can do this from the Web Services tab of the Preferences dialog box.
+
+\exercise{Changing the Layout of the Web Services Menu}{
+\label{changewsmenulayoutex}
+\exstep{Make sure you have loaded an alignment into Jalview, and examine the
+current layout of the alignment windowÕs Web Services menu.}
+\exstep{Open the preferences dialog box and select the web services tab.}
+\exstep{Ensure the ÔEnable JABAWS servicesÕ checkbox is selected, and unselect
+the ÔEnable Enfin ServicesÕ checkboxes.}
+\exstep{Hit ÔRefresh servicesÕ to update the web service menu -- once the
+progress bar has completed, open the web services menu to view the changes.}
+\exstep{Unselect the ÔIndex by hostÕ checkbox and refresh the services once again.
+
+{\sl Observe the way the layout of the JABAWS Alignment submenu changes.}
+}
+\exstep{Do the same with the ÔIndex by typeÕ checkbox.}
+}
+
+Jalview provides these options for configuring the layout of the web services
+menu because different Jalview users may have access to a different number of
+JABA services, and each will have their own preference regarding the layout of
+the menu.
+
+\begin{figure}[htbc]
+\begin{center}
+\includegraphics[width=3in]{images/jvjabawsconfig.pdf}
+\caption{{\bf The Jalview Web Services preferences panel.} Options are provided
+for configuring the list of JABA servers that Jalview will use, enabling and
+disabling Enfin services, and configuring the layout of the web services
+menu.}
+\end{center}
+\end{figure}
+
+\subsection{Running your own JABA server}
+You can download and run JABA on your own machine using the ÔVMWareÕ 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}{
+\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.
+
+{\bf Prerequisites}
+
+You will need a copy of VMWare Player/Workstation/Fusion on your machine.
+}
+
+\exstep{If you do not have VMWare player installed, download it from
+www.vmware.com (this takes a few minutes Ð you will need to register and wait
+for an email with a download link).}
+\exstep{Download the JABA virtual appliance archive called Ôjaba-vm.zipÕ from
+\textsf{http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip}
+
+WARNING: This is large ($~$300MB) and will take some time to download.
+}
+\exstep{Unpack the archiveÕs contents to a place on your machine with at least
+2GB of free space.
+
+(On windows, right click on the archive, and use the ÔExtract archive..Õ option).
+}
+\exstep{Open the newly extracted directory and double click the VMWare virtual
+machine configuration file (jabaws.vcf). This will launch the VMWare player.
+}
+\exstep{Once VMWare player has started up, it may ask the question Ôdid you move or copy
+this virtual appliance?Õ Ð select ÔcopyÕ.}
+\exstep{You may be prompted to download the VMWare linux tools Ð these are not
+necessary, so close the window or click on ÔlaterÕ}
+\exstep{You may also be prompted to install support for one or more devices (USB
+or otherwise) Ð say no to these options.}
+\exstep{Once the machine has loaded, it will display a series of IP addresses
+for the different services provided by the VM. Make a note of the JABAWS URL Ð
+this will begin with Ôhttp:Õ and end with Ô/jabawsÕ.}
+}
+
+\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
+menu.
+
+{\sl Alternately, use the System Java console if you have
+configured it to open when Jalview is launched, via your systemÕs Java
+preferences (under the ÔAdvancedÕ tab on Windows).}}
+\exstep{Open the preferences dialog and locate the Web Services preferences.}
+\exstep{Add the URL for the new JABAWS server you started in Exercise
+\ref{jabawsvmex} to the list of JABAWS urls using the ÔNew Service
+URLÕ button.}
+\exstep{You will be asked if you want to test the service. Hit ÔYesÕ to do this
+Ð- you should then see some output in the console window.
+
+{\sl Take a close look at the output in the console. What do you think is
+happening?}
+}
+\exstep{Hit {\sl OK} to save your preferences Ð- you have now added a new JABA
+service to Jalview!}
+\exstep{Try out your new JABA services by loading the ferredoxin sequences from
+http://www.jalview.org/tutorial/alignment.fa}
+\exstep{Launch an alignment using one
+of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the web services menu on the alignment window.
+
+{\sl Note: You can watch the JABA VM appliance's process working by opening the
+process monitor on your system. (On Windows XP, this involves right-clicking the
+system clock and opening the task manager Ð- then selecting the ÔProcessesÕ tab
+and sort by CPU).}
+}
+}
+
+
+\subsubsection{Resetting the JABA services setting to their defaults}
+Once you have configured a JABAWS server and selected the `OK' button of the
+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.
+
+\section{Multiple Sequence Alignment}
+\label{msaservices}
+Sequences can be aligned using a range of algorithms provided by JABA web
+services. These include ClustalW,\footnote{{\sl ``CLUSTAL W: improving the
+sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."} Thompson JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic
+Acids Research} {\bf 22}, 4673-80} Muscle,\footnote{{\sl ``MUSCLE: a multiple
+sequence alignment method with reduced time and space complexity"} Edgar, R.C.
+(2004) {\sl BMC Bioinformatics} {\bf 5}, 113} MAFFT,\footnote{{\sl ``MAFFT: a
+novel method for rapid multiple sequence alignment based on fast Fourier
+transform"} Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) {\sl
+Nucleic Acids Research} {\bf 30}, 3059-3066. and {\sl ``MAFFT version 5:
+improvement in accuracy of multiple sequence alignment"} Katoh, K., Kuma, K.,
+Toh, H. and Miyata, T. (2005) {\sl Nucleic Acids Research} {\bf 33}, 511-518.}
+ProbCons\footnote{PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
+Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
+(2005) {\sl Genome Research} {\bf 15} 330-340.} and T-COFFEE.\footnote{T-Coffee:
+A novel method for multiple sequence alignments. (2000) Notredame,Higgins and Heringa {\sl JMB} {\bf 302} 205-217} Of these,
+T-COFFEE is the slowest, but also the most accurate. ClustalW is historically the most widely used. Muscle is faster than ClustalW and probably the most accurate for smaller alignments and MAFFT is probably the best for large
+alignments\footnote{Clustal Omega, which was released in 2011, is arguably the
+fastest and most accurate tool for protein multiple alignment, and is
+included in JABAWS 2.0.}.
To run an alignment web service, select the appropriate method from the {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ \ldots} submenu (Figure
-\ref{webservices}). A progress window will appear giving information about the
-job and any errors that occur. After successful completion of the job, a new
-window is opened with the results, in this case an alignment. By default, the
-new alignment will be ordered in the same way as the input sequences;
-however, many alignment programs re-order the input to place homologous
-sequences close together. This ordering can be recovered using the 'Original
-ordering' entry within the {\sl Calculation $\Rightarrow$ Sort } sub menu.
+\ref{webservices}). For each service you may either perform an alignment with
+default settings, use one of the available presets, or customise the parameters
+with the `{\sl Edit and Run ..}' dialog box. Once the job is submitted, a
+progress window will appear giving information about the job and any errors that
+occur. After successful completion of the job, a new window is opened with the
+results, in this case an alignment. By default, the new alignment will be
+ordered in the same way as the input sequences; however, many alignment programs
+re-order the input to place homologous sequences close together. This ordering
+can be recovered using the `Original ordering' entry within the {\sl Calculation
+$\Rightarrow$ Sort } sub menu.
\begin{figure}[htbp]
\begin{center}
If the view or selected region that is submitted for alignment contains hidden regions, then only the visible sequences will be submitted to the service. Furthermore, each contiguous segment of sequences will be aligned independently (resulting a number of alignment `subjobs' appearing in the status window). Finally, the results of each subjob will be concatenated with the hidden regions in the input data prior to their display in a new window. This approach ensures that 1) hidden column boundaries in the input data are preserved in the resulting alignment - in a similar fashion to the constraint that hidden columns place on alignment editing (see Section \ref{lockededits}). 2) hidden columns can be used to preserve existing parts of an alignment whilst the visible parts are locally refined.
\exercise{Multiple Sequence Alignment}{
-\exstep{ Close all windows and open the alignment at {\sf http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle Multiple Protein Sequence Alignment}. A window will open giving the job status. After a short time, a second window will open with the results of the alignment.}
-\exstep{Select the first sequence set by clicking on the window and try running ClustalW and MAFFT (from the {\sl Web Services $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and you should notice small differences.
-}
+\exstep{ Close all windows and open the alignment at {\sf
+http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
+Web Service $\Rightarrow$ Alignment $\Rightarrow$ Default Settings} for Muscle. A window will open giving the job status. After a short time, a second window will open with the results of the alignment.} \exstep{Select the first sequence set by clicking on the window and try running ClustalW and MAFFT (from the {\sl Web Services $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and you should notice small differences. }
\exstep{Select the last three sequences in the MAFFT alignment, and de-align them with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect them and then submit the view for re-alignment with ClustalW.}
\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment. Once the ClustalW re-alignment has completed, compare the results of re-alignment of the three sequences with their alignment in the original MAFFT result.}
\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them. Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ MAFFT} to submit the visible portion of the alignment to MAFFT. When the web service job pane appears, note that there are now two alignment job status panes shown in the window.}
}
-\subsection{Protein Secondary Structure Prediction}
+\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
+usually able to modify the following types of parameters:
+\begin{list}{$\bullet$}{}
+\item Amino acid or nucleotide substitution score matrix
+\item Gap opening and widening penalties
+\item Types of distance metric used to construct guide trees
+\item Number of rounds of re-alignment or alignment optimisation
+\end{list}
+
+
+\subsubsection{Getting help on the parameters for a service}
+Each parameter available for a method usually has a short description, which
+jalview will display as a tooltip, or as a text pane that can be opened under
+the parameterÕs controls. In the parameter shown in Figure
+\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
+service can also be accessed, by right clicking the button and selecting a URL
+from the pop-up menu that will open.
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2.5in]{images/clustalwparamdetail.pdf}
+\caption{{\bf ClustalW parameter slider detail}. From the ClustalW {\sl Edit &
+Run ..} dialog box. }
+\label{clustalwparamdetail}
+\end{center}
+\end{figure}
+
+\subsection{Alignment Presets}
+The different multiple alignment algorithms available from JABA vary greatly in
+the number of adjustable parameters, and it is often difficult to identify what
+are the best values for the sequences that you are trying to align. For these
+reasons, each JABA service may provide one or more presets Ð which are
+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 Protein alignments (fastest speed)
+\item Nucleotide alignments (fastest speed)
+\end{list}
+
+The presets are displayed in the JABA web services submenu, and can also
+accessed from the parameter editing dialog box, which is opened by selecting
+the Ô{\sl Edit and run..}Õ option from the web serviceÕs menu. If you have used
+a preset, then it will be mentioned at the beginning of the job status file shown
+in the web service job progress window.
+
+\subsubsection{Alignment Service Limits}
+Multiple alignment is a computationally intensive calculation. Some JABA server
+services and service presets only allow a certain number of sequences to be
+aligned Ð the precise number will depend on the server that you are using to
+perform the alignment. Should you try to submit more sequences than a service
+can handle, then an error message will be shown informing you of the maximum
+number allowed by the server.
+
+\subsection{User defined Presets}
+Jalview allows you to create your own presets for a particular service. To do
+this, select the `{\sl Edit parameters and run ..}' option for your service,
+which will open a parameter editing dialog box like the one shown in Figure
+\ref{jwsparamsdialog}.
+
+The top row of this dialog allows you to browse the existing presets, and
+when editing a parameter set, allows you to change its nickname. As you
+adjust settings, buttons will appear at the top of the parameters dialog that
+allow you to create, update, delete or undo changes to the currently selected
+user preset. In addition to the parameter set name, you can also provide a short
+description for the parameter set, which will be shown in the tooltip for the
+parameter set's entry in the web services menu.
+
+\begin{figure}[htbc]
+\center{
+\includegraphics[width=3in]{images/jvaliwsparamsbox.pdf}
+\caption{{\bf Jalview's JABA alignment service parameter editing dialog box}.}
+\label{jwsparamsdialog} }
+\end{figure}
+
+\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,
+it will show your custom preset amongst the options available for running the
+JABA service.
+
+%
+% \exercise{Creating and using user defined presets}{\label{createandusepreseex}
+% \exstep{Import the file at
+% \textsf{http://www.jalview.org/tutorial/fdx\_unaligned.fa} into jalview.}
+% \exstep{Use the `{\slDiscover Database Ids}' function to recover the PDB cross
+% references for the sequences.}
+% \exstep{Align the sequences using the default ClustalW parameters.}
+% \exstep{Use the `{\sl Edit and run..}'
+% option to open the ClustalW parameters dialog box, and create a new preset using
+% the following settings:
+% \begin{list}{$\bullet$}{}
+% \item BLOSUM matrix (unchanged)
+% \item Gap Opening and End Gap penalties = 0.05
+% \item Gap Extension and Separation penalties = 0.05
+% \end{list}
+%
+% As you edit the parameters, buttons will appear on the dialog box
+% allowing you revert your changes or save your settings as a new parameter
+% set.
+%
+% Before you save your settings, remeber to give them a meaningful name by editing
+% the text box at the top of the dialog box.
+% }
+% \exstep{Repeat the alignment using your new parameter set by selecting it from
+% the {\sl ClustalW Presets menu}.}
+% \exstep{These sequences have PDB structures associated with them, so it is
+% possible to compare the quality of the alignments.
+%
+% Use the {\sl View all {\bf N}
+% structures} option to calculate the superposition of 1fdn on 1fxd for both
+% alignments (refer to section \ref{superposestructs} for instructions). Which
+% alignment gives the best RMSD ? }
+% \exstep{Apply the same alignment parameter settings to the example alignment
+% (available from \textsf{http://www.jalview.org/examples/uniref50.fa}).
+%
+% Are there differences ? If not, why not ?
+% }
+% }
+
+
+\section{Protein Secondary Structure Prediction}
+\label{protsspredservices}
Protein secondary structure prediction is performed using the
Jpred\footnote{{\sl ``The Jpred 3 Secondary Structure Prediction Server''} Cole, C., Barber, J. D. and Barton, G. J. (2008) {\sl Nucleic Acids Research} {\bf 36}, (Web Server Issue) W197-W201
Select and hide some columns in one of the profiles that were returned from the JNet service, and then submit the profile for prediction again.
}
\exstep{
-When you get the result, verify that the prediction has not been made for the hidden parts of the profile, and that the JPred reliability scores differ from the prediction made on the full profile.
+When you get the result, verify that the prediction has not been made for the
+hidden parts of the profile, and that the JPred reliability scores differ from the prediction made on the full profile.
{\sl Note: you may want to keep this data for use in exercise \ref{viewannotfileex}.}
}
\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{
-Enter a suitable Sequence Feature Name (e.g. "Iron binding site") in the appropriate box. Click on the Feature Colour bar to change the colour if desired, add a short description ("One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences.
-}
-\exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at position 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
+Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
+appropriate box. Click on the Feature Colour bar to change the colour if
+desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at position 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
}
\exstep{
Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
\exstep{Select {\sl View $\Rightarrow$ Feature Settings\ldots} from the
alignment window menu. The Sequence Feature Settings window will appear. Move
this so that you can see the features you have just created. Click the check
-box for "Iron binding site" under {\sl Display} and note that display of this
+box for ``Iron binding site" under {\sl Display} and note that display of this
feature type is now turned off. Click it again and note that the features are
now displayed. Close the sequence feature settings box by clicking {\sl OK} or
{\sl Cancel}.} }
\end{figure}
\exercise{Annotating alignments}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} to bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}. Enter "Iron binding site" and click {\sl OK}. A new, empty, row appears.
+\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} to bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}. Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
}
\exstep{
-Navigate to column 97. Select column 97 on the new annotation row. Right click on the selection and select {\sl Label} from the context menu. Enter "Fe" in the box and click {\sl OK}. Right-click on the selection again and select {\sl Colour}. Choose a colour from the colour chooser dialogue and click {\sl OK}. Press [ESC] to remove the selection.
+Navigate to column 97. Select column 97 on the new annotation row. Right click on the selection and select {\sl Label} from the context menu. Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again and select {\sl Colour}. Choose a colour from the colour chooser dialogue and click {\sl OK}. Press [ESC] to remove the selection.
}
-\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the context menu. You will be prompted for a label. Enter "B" and press OK. A new line showing the sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet arrow.
+\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet arrow.
}
\exstep{Right click on the annotation row that you just created. Select {\sl Export Annotation} and, in the {\bf Export Annotation} dialog box that will open, select the Jalview format and click the [To Textbox] button.
\exercise{Retrieving features with DAS}{
\label{dasfeatretrexcercise}
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View $\Rightarrow$ Sequence Features\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment.
-}
-\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
+$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
+the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment. } \exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window. }
\exstep{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}
features using a graduated colourscheme in order to highlight these variations.
In order to apply a graduated scheme to a feature type, select the `Graduated
colour' entry in the Sequence feature type's popup menu, which is opened by
-right-clicking the feature type's color in the settings dalog box. Two types
+right-clicking the feature type's color in the settings dialog box. Two types
of colouring styles are currently supported: the default is quantitative
colouring, which shades each feature based on its score, with the highest
-scores receiving the 'Max' colour, and the lowest scoring features coloured
-with the 'Min' colour. Alternately, you can select the `Colour by label'
+scores receiving the `Max' colour, and the lowest scoring features coloured
+with the `Min' colour. Alternately, you can select the `Colour by label'
option to create feature colours according to the description text associated
with each feature. This is useful for general feature types - such as
-Uniprot's 'DOMAIN' feature - where the actual type of domain is given in the
+Uniprot's `DOMAIN' feature - where the actual type of domain is given in the
feature's description.
Graduated feature colour schemes can also be used to exclude low or
\subsection{Using features to re-order the alignment}
\label{featureordering}
-The presence of sequence features on certain seqences or in a particular
+The presence of sequence features on certain sequences or in a particular
region of an alignment can quantitatively identify important trends in
the aligned sequences. In this case, it is more useful to
re-order the alignment based on the number of features or their associated scores, rather than simply re-colour the aligned sequences. The sequence feature settings
-dialog box provides buttons two buttons, `Seq sort by Density' and `Seq sort by
-Score' that allow you to reorder the alignment according to the number of
+dialog box provides two buttons: `Seq sort by Density' and `Seq sort by
+Score', that allow you to reorder the alignment according to the number of
sequence features present on each sequence, and also according to any scores
associated with a feature. Each of these buttons uses the currently displayed
features to determine the ordering, but
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'.}}
+{\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
\subsubsection{Aligning Nucleic Acid Sequences}
Jalview only has limited knowledge of the capabilities of the programs that
-are made available to it {\sl via} web services. In particular, only the
-ClustalW and MAFFT programs will successfuly recognise and align nucleic acid
-sequences. MAFFT will also choose an appropriate parameter model. Whilst
-Muscle may appear to align DNA, it simply treats the base symbols as
-amino-acids, often leading to a poor quality alignment. Furthermore, it will
-almost certainly fail to align RNA containing Uracil bases, since `U' is not a
-valid one-letter amino acid code.
+are made available to it {\sl via} web services, so it is up to you, the user,
+to decide which service to use when working with nucleic acid sequences. The
+table below shows which alignment programs are appropriate for nucleotide alignment.
+
+\begin{table}{}
+\centering
+\begin{tabular}{|l|c|l|}
+Program& NA support& Notes\\
+\hline
+ClustalW& Yes&\begin{minipage}[f]{3in}
+Default is to autodetect nucleotide
+sequences. Editable parameters include nucleotide substitution matrices and
+distance metrics.
+\end{minipage}
+\\
+\hline
+Muscle& Yes (treat U as T)&\begin{minipage}[f]{3in}
+Default is to autodetect nucleotide
+sequences. Editable parameters include nucleotide substitution matrices and
+distance metrics.
+\end{minipage}
+\\
+\hline
+MAFFT& Yes&\begin{minipage}[f]{3in}
+Will autodetect nucleotide sequences and use a hardwired substitution model
+(all amino-acid sequence related parameters are ignored). Unknown whether
+substitution model treats Uracil specially.
+\end{minipage}
+\\
+\hline
+ProbCons& No&\begin{minipage}[f]{3in}
+ProbCons has no special support for aligning nucleotide sequences. Whilst an
+alignment will be returned, it is unlikely to be reliable.
+\end{minipage}
+\\
+\hline
+T-COFFEE& Yes&\begin{minipage}[f]{3in}
+Sequence type is automatically detected and an appropriate
+parameter set used as required. A range of nucleotide specific
+score models are available.\end{minipage}
+\\
+\end{tabular}
+\caption{{\bf JABAWS Alignment programs suitable for aligning nucleic acid
+sequences.} All JABAWS alignment services will return an alignment if provided
+with RNA or DNA sequences, with varying reliability. No programs include
+support for taking RNA secondary structure prediction into account when
+aligning sequences.}
+\label{nucleomsatools}
+\end{table}
\subsection{Translate cDNA}
git://source.jalview.org / jalview-manual.git / blobdiff