\usepackage[format=hang,margin=10pt]{caption}
\usepackage{footnote}
\usepackage{graphicx}
-\usepackage{amssymb}
+\usepackage{fouriernc}
+%\usepackage{amssymb}
\usepackage{epstopdf}
\usepackage{hyperref}
\usepackage{subfigure}
{\Huge
-Jalview 2.7
+Jalview 2.8.2
}
\vspace{0.5in}
{\huge
-A manual and introductory tutorial }
+A Manual with Introductory Tutorial }
\vspace{2.4in}
{\large
-David Martin, James Procter, Andrew Waterhouse, Saif Shehata and Geoff Barton
+David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,
+Suzanne Duce and Geoff Barton
+
}
\vspace{2in}
-Manual version 1.3.02
+Manual Version 1.5
+% post CLS lifesci course on 15th January
+% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-25th June 2012
+4th December 2014
\end{center}
-\newpage
+%\newpage
-% \clearemptydoublepage
+\clearemptydoublepage
% ($Revision$) 11th October 2010.}
% TODO revise for 2.6
\subsection{Jalview}
Jalview is a multiple sequence alignment viewer, editor and analysis tool.
Jalview is designed to be platform independent (running on Mac, MS Windows, Linux
-and any other platform that supports Java), capable of editing and analysing
-large alignments (thousands of sequences) with minimal degradation in
+and any other platforms that supports Java). Jalview is capable of editing and
+analysing large alignments (thousands of sequences) with minimal degradation in
performance, and able to show multiple integrated views of the alignment and
other data. Jalview can read and write many common sequence formats including
FASTA, Clustal, MSF(GCG) and PIR.
analysis capabilities. The {\bf JalviewLite} applet has the same core
visualization, editing and analysis capabilities as the desktop, without the
desktop's webservice and figure generation capabilities. It is designed to be
-embedded in a web page\footnote{A demonstration version of Jalview (Jalview Micro
+embedded in a web page,\footnote{A demonstration version of Jalview (Jalview Micro
Edition) also runs on a mobile phone but the functionality is limited to sequence
-colouring.}, to allow customisable display of alignments for web sites such as
-{\bf pfam}\footnote{\url{http://pfam.sanger.ac.uk}}.
+colouring.} and includes a javascript API to allow customisable display of alignments for web sites such as
+{\bf Pfam}.\footnote{\url{http://pfam.sanger.ac.uk}}
-Jalview 2.7 was released in September 2011. The Jalview Desktop in this version
-provides access to sequence, alignment and protein structure databases, and
-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
+Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
+provides access to protein and nucleic acid sequence, alignment and structure
+databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
+\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. A
+Distributed Annotation System (DAS) client\footnote{jDAS - released under Apache license (v2.0) at \url{http://code.google.com/p/jdas}} 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.
+provides a graphical user interface for the multiple sequence alignment, conservation analysis and protein disorder prediction methods provided as {\bf Ja}va {\bf B}ioinformatics
+{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS). JABAWS\footnote{released under GPL at \url{http://www.compbio.dundee.ac.uk/jabaws}} is a system for running bioinformatics programs that you can download and run on your own machine or cluster, or install on compute clouds.
\subsection{Jalview's Capabilities}
% TODO add references to appropriate sections for each capability described here.
-Figure \ref{jvcapabilities} gives an overview of the main features of the Jalview desktop application. Its primary function is the editing and visualization of sequence alignments, and their interactive analysis. Tree building, principal components analysis, physico-chemical property conservation and sequence consensus analyses are built in to the program. Web services enable Jalview to access remote alignment and secondary structure prediction programs, as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
+Figure \ref{jvcapabilities} gives an overview of the main features of the
+Jalview desktop application. Its primary function is the editing and
+visualization of sequence alignments, and their interactive analysis. Tree
+building, principal components analysis, physico-chemical property conservation
+and sequence consensus analyses are built into the program. Web services enable
+Jalview to access on line alignment and secondary structure prediction programs,
+as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5.8in]{images/jvcapabilities.pdf}
between Jalview, TOPALi and AstexViewer.} in 2004, enabling Andrew Waterhouse and
Jim Procter to re-engineer the original program to introduce contemporary developments
in bioinformatics and take advantage of the latest web and Java technology.
-Jalview's development is now supported for a further 5 years from October 2009
-by an award from the BBSRC's Tools and Resources fund. In 2010 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.
+Jalview's development was supported from 2009
+by an award from the BBSRC's Tools and Resources fund. Jalview's development is
+currently being funded by a BBSRC `Extending The Jalview Resource for
+Biological Sequence Alignment and Analysis' grant and a Wellcome Trust
+`Extending The Jalview Resource for Biological Sequence Alignment and Analysis'
+grant. In 2010, 2011, and 2012, Jalview benefitted from the
+\href{http://code.google.com/soc/}{Google Summer of Code}, when Lauren Lui and Jan Engelhardt introduced new features for handling RNA alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
%TODO describe future plans in history ? not a good idea.
\subsubsection{Citing Jalview}
If you use Jalview in your work you should cite:\newline
-{\sl ``Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"}\newline
-Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) \newline {\sl Bioinformatics} doi: 10.1093/bioinformatics/btp033
+{\sl "Jalview Version 2 - a multiple sequence alignment editor and analysis
+workbench"}\newline Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) \newline {\sl Bioinformatics} doi: 10.1093/bioinformatics/btp033
-This paper supersedes the original Jalview publication:\newline {\sl ``The Jalview Java alignment
-editor"} \newline Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey J. Barton (2004) \newline {\sl Bioinformatics} {\bf 20} 426-427.
+This paper supersedes the original Jalview publication:\newline {\sl "The
+Jalview Java alignment editor"} \newline Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey J. Barton (2004) \newline {\sl Bioinformatics} {\bf 20} 426-427.
-\subsection{About this tutorial }
+\subsection{About this Tutorial }
This tutorial is written in a manual format with short exercises where
appropriate, typically at the end of each section. This chapter concerns the
-basic operation of Jalview and should be sufficient for those who just want to
+basic operation of Jalview and should be sufficient for those who want to
load Jalview (Section \ref{startingjv}), open an alignment (Section \ref{loadingseqs}), perform basic editing and colouring (Section \ref{selectingandediting} and Section \ref{colours}), and produce publication
and presentation quality graphical output (Section \ref{layoutandoutput}).
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.
+specific features of use when working with nucleic acid sequences, such as translation and linking to protein
+coding regions, and the display and analysis of RNA secondary structure.
%^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
\subsubsection{Typographic Conventions}
-Keystrokes using the special non-symbol keys are represented in the tutorial by enclosing the pressed keys with square brackets ({\em e.g.} [RETURN] or [CTRL]). Keystroke combinations are combined with a `-' symbol ({\em e.g.} [CTRL]-C means press [CTRL] and the `C' key). Menu options are given as a path from the menu that contains them - for example {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} means to select the `From URL' option from the `Input Alignment' submenu of a window's `File' dropdown menu.
+Keystrokes using the special non-symbol keys are represented in the tutorial by
+enclosing the pressed keys with square brackets ({\em e.g.} [RETURN] or [CTRL]).
+
+Keystroke combinations are combined with a `-' symbol ({\em e.g.} [CTRL]-C means
+press [CTRL] and the `C' key).
+
+Menu options are given as a path from the menu
+that contains them - for example {\sl File $\Rightarrow$ Input Alignment
+$\Rightarrow$ From URL} means to select the `From URL' option from the `Input
+Alignment' submenu of a window's `File' dropdown menu.
-\section{Obtaining and starting The Jalview Desktop Application}
+\section{Obtaining and Starting the Jalview Desktop Application}
\label{startingjv}
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/download.pdf}
-\caption{{\bf Download page on the Jalview web site}}
+\caption{\bf Download page on the Jalview web site at www.jalview.org.}
\label{download}
\end{center}
\end{figure}
-This tutorial is based on the application version of Jalview, the Jalview
-Desktop. Much of the information will also be useful for users of the JalviewLite
-applet, which has the same core editing, analysis and visualization capabilities (see the
+This tutorial is based on the Jalview
+Desktop application. Much of the information will also be useful for users of
+the JalviewLite applet, which has the same core editing, analysis and visualization capabilities (see the
\href{http://www.jalview.org/examples/applets.html}{JalviewLite Applet Examples}
page for examples). The Jalview Desktop, however, is much more powerful, and
includes additional support for interaction with external web services, and
production of publication quality graphics.
The Jalview Desktop can be run in two ways; as an application launched from the
-web {\sl via} Java Web Start, or as an application loaded onto your hard drive. Both
-versions are obtained from the Download page at the Jalview web site
-(http://www.jalview.org/).
-
-Jalview can be started directly with webstart by navigating to the Download page
-({\sl via} the menu on the left hand side), and clicking the `Start with Java Webstart'
-button. (Figure \ref{download}). This will always launch the latest stable
-release of Jalview.\par
-
-The application will start automatically though you may be prompted to accept a
-security certificate signed by the Barton Group. You can always trust us, so click trust
-or accept as appropriate. The splash screen (Figure \ref{splash}) gives
-information about the version and build date that you are running,
+web {\sl via} Java webstart, or as an application loaded onto your hard drive.
+The webstart version is launched from the pink `Launch Jalview Desktop
+button' at the top right handside of pages of the website
+\href{http://www.jalview.org}{(www.jalview.org)}.
+To download the locally installable version, follow the links on the download
+page
+\href{http://www.jalview.org/download}{(www.jalview.org/download) }
+ (Figure \ref{download}).
+These links will launch the latest stable release of Jalview.\par
+
+When the application is launched with webstart, two dialogs may appear before
+the application starts. If your browser is not set up to handle webstart, then
+clicking the launch link may download a file that needs to be opened
+manually, or prompt you to select the correct program to handle the webstart
+file. If that is the case, then you will need to locate the {\bf javaws} program
+on your system\footnote{The file that is downloaded will have a type of {\bf
+application/x-java-jnlp-file} or {\bf .jnlp}. The {\bf javaws} program that can run
+this file is usually found in the {\bf bin} directory of your Java
+installation}. Once java webstart has been launched, you may also be prompted to
+accept a security certificate signed by the Barton Group.\footnote{On some
+systems, the certificate may be signed by 'UNKNOWN'. In this case, clicking
+through the dialogs to look at the detailed information about the certificate
+should reveal it to be a Barton group certificate.} You can always trust us, so
+click trust or accept as appropriate. The splash screen (Figure \ref{splash})
+gives information about the version and build date that you are running,
information about later versions (if available), and the paper to cite in your
-publications. This information is also available on the Jalview web site and from the {\sl Help $\Rightarrow$ About} menu option.
+publications. This information is also available on the Jalview web site at
+\url{http://www.jalview.org}.
%[fig 2]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/splash.pdf}
-\caption{{\bf Jalview splash screen}}
+\caption{{\bf Jalview splash screen.}}
\label{splash}
\end{center}
\end{figure}
When Jalview starts it will automatically load an example alignment from the
-Jalview site. This behaviour can be changed in the Jalview Desktop preferences
-dialog opened from the Desktop's {\sl Tools $\Rightarrow$ Preferences..} menu.
-This alignment will look like the one in Figure \ref{startpage} (this is taken
+Jalview site. This behaviour can be switched off in the Jalview Desktop
+preferences dialog by unchecking the open file option.
+This alignment will look like the one in Figure \ref{startpage} (taken
from Jalview version 2.7).
%[figure 3 ]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4in]{images/start.pdf}
-\caption{{\bf Default startup for Jalview}}
+\caption{{\bf Default startup for Jalview.}}
\label{startpage}
\end{center}
\end{figure}
\subsubsection{Jalview News RSS Feed}
-From time to time, important announcements are made available to users of the
-Jalview Destop {\sl via} the Jalview News reader. This window will open
+Announcements are made available to users of the
+Jalview Desktop {\sl via} the Jalview News reader. This window will open
automatically when new news is available, and can also be accessed {\sl via} the
-Desktop's `{\sl Tools $\Rightarrow$ Show Jalview News}' menu entry.
+Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry.
\begin{figure}[htbp]
\begin{center}
\end{figure}
-\exercise{Starting Jalview}{
+\exercise{Launching Jalview from the Jalview website}{
\label{start}
-\exstep{Point your web browser at the \href{http://www.jalview.org}{Jalview web site} and start Jalview by clicking on the `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 \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. } }
+\exstep{Open the Jalview web
+site \href{http://www.jalview.org}{(www.jalview.org)}
+in your web browser. Launch Jalview by clicking on the
+pink `Launch Jalview' Desktop button in the top right hand corner. This
+will download and open a jalview.jnlp webstart file.} \exstep {Dialogue boxes
+will open and ask if you want to open the the jalview.jnlp file as the file is an application downloaded from the
+Internet, click Open. (Note you maybe asked to update Java, if you agree then it
+will automatically update the Java software). As Jalview opens, four demo
+Jalview windows automatically load.} \exstep {If
+you are having trouble, it may help changing the browser you are using, as the browsers and
+it's version may effect this process.}
+\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
+to the {\sl Tools $\Rightarrow$
+Preferences...} menu on the desktop. A `Preference'
+dialogue box opens, untick the box adjacent to the `Open file' entry in the
+`Visual' preferences tab.
+Click OK to save the preferences.}
+\exstep{Launch another Jalview workbench from the web site by clicking on the
+pink Launch button.
+The example alignment should not be loaded as Jalview starts up.}
+\exstep{To reload the original demo file select the
+{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
+the URL history button on the right hand side of the dialog box to view the
+files, selected exampleFile-2-7.jar, then click OK.}
+{\bf Note:} Should you want to reload the example alignment or load your own
+sequence during the launch process, then go
+to the {\sl Tools $\Rightarrow$
+Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
+preferences tab, type in the URL of the sequence you want to load. This
+file will load during the start up process.\\
+
+As the jalview.jnlp file launches Jalview on your desktop, you
+may want to move this from the downloads folder to another folder.
+Opening from this file will allow Jalview to be launched offline.
+
+{\bf Help launching Jalview is avaliable in a video on
+\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
+the website.}}
\subsection{Getting Help}
\label{gettinghelp}
\subsubsection{Built in documentation}
-Jalview has comprehensive on-line help documentation. Select {\sl Help $\Rightarrow$ Documentation} from the main window menu and a new window will open (Figure \ref{help}). The appropriate topic can then be selected from the navigation panel on the left hand side. To search for a specific topic, click the `search' tab and enter keywords in the box which appears.
+Jalview has comprehensive on-line help documentation. Select {\sl Help
+$\Rightarrow$ Documentation} from the main window menu and a new window will
+open (Figure \ref{help}). The appropriate topic can then be selected from the
+navigation panel on the left hand side. To search for a specific topic, click
+the `search' tab and enter keywords in the box which appears.
\begin{figure}[htbp]
\begin{center}
\parbox[c]{2in}{\centerline{\includegraphics[width=2.75in]{images/help1.pdf}}}
\parbox[c]{4in}{\includegraphics[width=4in]{images/help2.pdf}}
-\caption{{\bf Accessing the built in Jalview documentation}}
+\caption{{\bf Accessing the built in Jalview documentation.}}
\label{help}
\end{center}
\end{figure}
\subsubsection{Email lists}
-The Jalview Discussion list {\tt jalview-discuss@jalview.org} provides a forum for Jalview users and developers to raise problems and exchange ideas - any problems, bugs, and requests for help should be raised here. The {\tt jalview-announce@jalview.org} list can also be subscribed to if you wish to be kept informed of new releases and developments. Archives and mailing list subscription details can be found on the Jalview web site.
+The Jalview Discussion list {\tt jalview-discuss@jalview.org} provides a forum
+for Jalview users and developers to raise problems and exchange ideas - any
+problems, bugs, and requests for help should be raised here. The {\tt
+jalview-announce@jalview.org} list can also be subscribed to if you wish to be
+kept informed of new releases and developments.
+
+Archives and mailing list
+subscription details can be found in the Jalview web site's \href{http://www.jalview.org/community}{community section}.
\section{Navigation}
\label{jvnavigation}
The major features of the Jalview Desktop are illustrated in Figure \ref{anatomy}. The alignment window is the primary window for editing and visualization, and can contain several independent views of the alignment being worked with. The other windows (Trees, Structures, PCA plots, etc) are linked to a specific alignment view. Each area of the alignment window has a separate context menu accessed by clicking the right mouse button.
- Jalview has two navigation and editing modes: normal mode, where editing and navigation is performed using the mouse, and cursor mode where editing and navigation are performed using the keyboard. The F2 key is used to switch between these two modes.
+ Jalview has two navigation and editing modes: {\bf normal mode}, where
+ editing and navigation is performed using the mouse, and {\bf cursor mode}
+ where editing and navigation are performed using the keyboard. The {\bf F2 key}
+ is used to switch between these two modes. With a Mac as the F2 is
+ often assigned to screen brightness, one maay often need to type {\bf function
+ [Fn] key with F2}.
\begin{figure}[htb]
\begin{center}
\subsection{Navigation in Normal mode}
-Jalview always starts up in Normal mode, where the mouse is used to interact with the displayed alignment view. You can move about the alignment by clicking and dragging the ruler scroll bar to move horizontally, or by clicking and dragging the alignment scroll bar to the right of the alignment to move vertically. If all the rows or columns in the alignment are displayed, the scroll bars will not be visible.
-
- Each alignment view shown in the alignment window presents a window onto the visible regions of the alignment. This means that with anything more than a few residues or sequences, alignments can become difficult to visualize on the screen because only a small area can be shown at a time. It can help, especially when examining a large alignment, to have an overview of the whole alignment. Select {\sl View $\Rightarrow$ Overview Window} from the window menu (Figure \ref{overview}).
-%(Figure4)
+Jalview always starts up in Normal mode, where the mouse is used to interact
+with the displayed alignment view. You can move about the alignment by clicking
+and dragging the ruler scroll bar to move horizontally, or by clicking and
+dragging the alignment scroll bar to the right of the alignment to move
+vertically. If all the rows or columns in the alignment are displayed, the
+scroll bars will not be visible.
+
+ Each alignment view shown in the alignment window presents a window onto the
+ visible regions of the alignment. This means that with anything more than a few
+ residues or sequences, alignments can become difficult to visualize on the
+ screen because only a small area can be shown at a time. It can help,
+ especially when examining a large alignment, to have an overview of the whole
+ alignment. Select {\sl View $\Rightarrow$ Overview Window} from the Alignment
+ window menu bar (Figure \ref{overview}\footnote{the menu shown in this figure
+ is from Jalview 2.2, later versions have more options.}).
+% (Figure4)
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/overview.pdf}
-\caption{{\bf Alignment Overview Window}}
+\caption{{\bf Alignment Overview Window.} The overview window for a view is opened from the {\em View} menu.}
\label{overview}
\end{center}
\end{figure}
-The red box in the overview window shows the current view in the alignment window. A percent identity histogram is plotted below the alignment overview. Shaded parts indicate rows and columns of the alignment that are hidden (in this case, a single row at the bottom of the alignment - see Section \ref{hidingregions}). You can navigate around the alignment by dragging the red box. %Try this now and see how the view in the alignment window changes.
+The red box in the overview window shows the current view in the alignment
+window. A percent identity histogram is plotted below the alignment overview.
+Shaded parts indicate rows and columns of the alignment that are hidden (in this
+case, a single row at the bottom of the alignment - see Section
+\ref{hidingregions}). You can navigate around the alignment by dragging the red
+box.
+
+%Try this now and see how the view in the alignment window changes.
-\parbox[c]{3in}{Alignment and analysis windows are closed by clicking on the usual `close' icon (indicated by arrows on Mac OS X). If you want to close all the alignments and analysis windows at once, then use the {\sl Window $\Rightarrow$ Close All} option from the Jalview desktop (\em{warning: make sure you have saved your work because this cannot be undone !}). }
+\parbox[c]{3in}{Alignment and analysis windows are closed by clicking on the
+usual `close' icon (indicated by arrows on Mac OS X). If you want to close all
+the alignments and analysis windows at once, then use the {\sl Window
+$\Rightarrow$ Close All} option from the Jalview desktop.
+
+{\bf \em{Warning: make sure you have saved your work because this cannot be
+undone !}} }
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
\subsection{Navigation in Cursor mode}
\label{cursormode}
-\parbox[c]{5in}{Cursor mode navigation enables the experienced user to quickly and precisely navigate, select and edit parts of an alignment. On pressing F2 to enter cursor mode the position of the cursor is indicated by a black background and white text. The cursor can be placed using the mouse or moved by pressing the arrow keys ($\uparrow$, $\downarrow$, $\leftarrow$, $\rightarrow$).
+\parbox[c]{5in}{Cursor mode navigation enables the user to quickly
+and precisely navigate, select and edit parts of an alignment. On pressing F2 to
+enter cursor mode the position of the cursor is indicated by a black background
+and white text. The cursor can be placed using the mouse or moved by pressing
+the arrow keys ($\uparrow$, $\downarrow$, $\leftarrow$, $\rightarrow$).
}\parbox[c]{1.25in}{\centerline{\includegraphics[width=0.8in]{images/cursor1.pdf}}}
Rapid movement to specific positions is accomplished as listed below:
\exercise{Navigation}{
\label{navigate}
+Jalview has two navigation and editing modes: {\bf normal} mode (where editing
+and navigation are via the mouse) and the {\bf cursor} mode (where editing and
+navigation are via the keyboard).
+The {\bf F2 key} is used to switch between these two modes. With a Mac often
+need to type function {\bf Fn key and F2}, as button is often assigned to
+screen brightness. Jalview always starts up in {\bf normal mode}.
+
+\exstep{Load an example alignment from its URL
+(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
+using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} dialog
+box.
+(The URL should be stored in its history and clicking on the {\sl down arrow} is
+an easy way to access it.)}
\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
-\exstep{Find and open the Overview Window. Move around the alignment by clicking and dragging the red box in the overview window.}
-\exstep{Look at the status bar as you move the mouse over the alignment. It should indicate information about the sequence and residue under the cursor.
-}
-\exstep{Press [F2] to enter Cursor mode. Use the arrow keys to move the cursor around the alignment.
-Move to sequence 7 by pressing {\sl 7 S}. Move to column 18 by pressing {\sl 1 8 C}. Move to residue 18 by pressing {\sl 1 8 P}. Note that these can be two different positions if gaps are inserted into the sequence. Move to sequence 5, column 13 by typing {\sl 1 3 , 5 [RETURN]}.
-}
-}
+\exstep{Find the Overview Window, {\sl Views
+$\Rightarrow$ Overview Window} and open it. Move around the
+alignment by clicking and dragging the red box in the overview window.}
+\exstep{Look at the status bar (lower left hand corner of the alignment window) as
+you move the mouse over the alignment. It indicates information about the
+sequence and residue under the cursor.}
+\exstep{Press [F2] to enter {\bf Cursor mode}. Use the direction {\bfarrow
+keys} to move the cursor around the alignment.}
+\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
+{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
+two different positions if gaps are inserted into the sequence. Move to sequence 5,
+column 13 by typing {\bf 1 3 , 5 [RETURN]}.}
+
+{\bf Note:} To view Jalview's comprehensive on-line help documentations select
+Help on desktop menu, clicking on Documentation will open a Documentation
+window. Select topic from the navigation panel on the left hand side or use the
+Search tab to select specific key words
+
+{\bf Help navigating Jalview is avaliable in a video on
+\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
+the website.}}
+
\subsection{The Find Dialog Box}
\label{searchfunction}
A further option for navigation is to use the {\sl Select $\Rightarrow$
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.
+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
-\section{Loading your own sequences}
+\section{Loading your Own Sequences}
\label{loadingseqs}
Jalview provides many ways to load your own sequences. %For this section of the tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
\subsection{Drag and Drop}
In most operating systems you can just drag a file icon from a file browser
- window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended
-to that alignment. Drag and drop also works when loading data from a URL -
+ window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended.
+ Drag and drop also works when loading data from a URL -
simply drag the link or url from the address panel of your browser on to an
alignment or the Jalview desktop background and Jalview will load data from the
URL directly.
\subsection{From a File}
- Jalview can read sequence alignments from a sequence alignment file. This is a text file, not a word processor document. For entering sequences from a wordprocessor document see Cut and Paste (Section \ref{cutpaste}) below. Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu (Figure \ref{loadfile}). You will then get a file selection window where you can choose the file to open. Remember to select the appropriate file type. Jalview can automatically identify some sequence file formats.
+Jalview can read sequence alignments from a sequence alignment file. This is a
+text file, not a word processor document. For entering sequences from a
+wordprocessor document see Cut and Paste (Section \ref{cutpaste}) below. Select
+{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main
+menu (Figure \ref{loadfile}). You will then get a file selection window where
+you can choose the file to open. Remember to select the appropriate file type.
+Jalview can automatically identify some sequence file formats.
%[fig 6]
\begin{figure}[htbp]
\end{figure}
\subsection{From a URL}
- Jalview can read sequence alignments directly from a URL. Please note that the files must be in a sequence alignment format - an HTML alignment or graphics file cannot be read by Jalview.
-Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and a window will appear asking you to enter the URL (Figure \ref{loadurl}). Jalview will attempt to automatically discover the file format.
+Jalview can read sequence alignments directly from a URL. Please note that the
+files must be in a sequence alignment format - an HTML alignment or graphics
+file cannot be read by Jalview.
+Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the
+main menu and a window will appear asking you to enter the URL (Figure
+\ref{loadurl}). Jalview will attempt to automatically discover the file format.
%[fig 7]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2in]{images/menuloadurl.pdf}
\includegraphics[width=3in]{images/loadurlbox.pdf}
-\caption{{\bf Opening an alignment from a URL }}
+\caption{{\bf Opening an alignment from a URL. }}
\label{loadurl}
\end{center}
\end{figure}
\begin{center}
\includegraphics[width=2in]{images/menuloadtext.pdf}
\includegraphics[width=3in]{images/loadtextbox.pdf}
-\caption{{\bf Opening an alignment from pasted text }}
+\caption{{\bf Opening an alignment from pasted text. }}
\label{loadtext}
\end{center}
\end{figure}
-\subsection{From a public database}
+\subsection{From a Public Database}
\label{fetchseq}
-Jalview can retrieve sequences and sequence alignments from the public
-databases housed at the European Bioinformatics Institute, such as Uniprot,
-Pfam and the PDB, as well as any DAS sequence server registered at the
-configured DAS registry. This facility avoids having to manually locate, save
-and load the sequences, and allows Jalview to gather additional metadata
-provided by the source, such as annotation and database cross references.
+Jalview can retrieve sequences and sequence alignments from the public databases
+housed at the European Bioinformatics Institute, including Uniprot, Pfam, Rfam
+and the PDB, as well as any DAS sequence server registered at the configured DAS
+registry. Jalview's sequence fetching capabilities allow you to avoid having to
+manually locate and save sequences from a web page before loading them into
+Jalview. It also allows Jalview to gather additional metadata provided by the
+source, such as annotation and database cross references.
Select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and
-a window will appear (Figure \ref{loadseq}). Use the menu box to select the
-appropriate database, enter one or several database IDs or accession numbers separated
- by a semicolon and press OK. Jalview will then attempt to retrieve them from the chosen database. Example queries are provided for some
-databases to test that a source is operational, and can also be used as a guide
-for the type of accession numbers understood by the source.
-%[fig 9]
+a window will appear (Figure \ref{loadseq}). Pressing the database selection
+button in the dialog box opens a new window showing all the database sources
+Jalview can access (grouped by the type of database). Once you've selected the
+appropriate database, hit OK close the database selection window, and then enter
+one or several database IDs or accession numbers separated by a semicolon and
+press OK. Jalview will then attempt to retrieve them from the chosen database.
+Example queries are provided for some databases to test that a source is
+operational, and can also be used as a guide for the type of accession numbers
+understood by the source.\footnote{Most DAS sources support {\em range queries}
+that can be used to download just a particular range from a sequence database
+record.}
+% [fig 9]
\begin{figure}[htbp]
\begin{center}
-\includegraphics[width=2.5in]{images/fetchseq.pdf}
-\caption{{\bf Retrieving sequences from a public database}}
+\includegraphics[width=5in]{images/fetchseq.pdf}
+\caption{{\bf Retrieving sequences from a public database.}}
\label{loadseq}
\end{center}
\end{figure}
\exercise{Loading sequences}{
\label{load}
-\exstep{Start Jalview then close all windows by selecting {\sl Window $\Rightarrow$ Close All} from the main menu.}
-\exstep{Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the main menu and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box. Click OK%jbp shouldn't this be sl
-and the alignment should load.
-}
-\exstep{Close all windows using the {\sl Window $\Rightarrow$ Close All} main
-menu option. Point your web browser at the same \href{http://www.jalview.org/tutorial/alignment.fa}{URL} and save the file to your desktop. Open this file in Jalview by selecting {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu and selecting the file from your desktop. Click OK and load the alignment.}
-\exstep{Select {\sl Window $\Rightarrow$ Close All} and drag the alignment.fa file from the desktop onto the Jalview window. The alignment should open. Try dragging onto an empty Jalview and onto an existing
-alignment and observe the results. You can also try dragging the
-\href{http://www.jalview.org/tutorial/alignment.fa}{URL} directly onto Jalview.
-}
-\exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the PFAM seed database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. }
-\exstep{Open the \href{http://www.jalview.org/tutorial/alignment.fa}{URL} above in a
-web browser. Select and copy the entire text to the clipboard (usually {\sl via} the
-browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running
-and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} .
+\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
+close all windows.}
+\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box.
+
+Click OK to load the alignment.}
+\exstep{{\bf Loading sequences from a file:} Close all windows using the
+{\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
+Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
+your web browser and {\bf save} the file to your desktop.
+
+Open the file you have just saved in Jalview by selecting {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu and
+selecting this file.
+Click OK to load the alignment.}
+\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+
+(i) Select {\sl Desktop $\Rightarrow$ Window
+$\Rightarrow$ Close All}. Then drag the alignment.fa file from the desktop and
+drop it onto the Jalview window, the alignment should open.
+
+Test the differences
+between (a) dragging the sequence onto the empty Jalview desktop and (b)
+dragging the sequence onto an existing alignment window.
+
+(ii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
+web browser. Drag the URL directly from browser window onto Jalview.
+
+(If the URL is downloaded instead of opened in the browser, then
+locate the file in your download directory and open it in a text editor.)
+
+(iii) Open the alignment.fa file using text editor. Copy the sequence text from the
+file into the clipboard and paste it into the desktop
+background by right-clicking and selecting Paste to new alignment option.
+
+(iv) In the text editor, copy the sequence text from
+alignment.fa into the clipboard (usually {\sl via} the browser's {\sl Edit
+$\Rightarrow$ Copy} menu option). In the Desktop menu, select {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
Paste} text box menu option. Click {\sl New Window} and the alignment will be
-loaded. } }
+loaded.}
+\exstep{{\bf Loading sequences from Public Database:} Select {\sl File
+$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
+called New Sequence Fetcher.
+Press database selection button at the top of the dialog box, this opens
+another window called Select Database Retrieval Source showing all the database
+sources.
+
+Select the {\bf PFAM seed} database and click ok, then enter the accession
+number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
+
+Several database IDs
+or accession numbers can be loaded by using semicolons to separated them.}}
\subsection{Memory Limits}
\label{memorylimits}
-Jalview is a Java program. One unfortunate implication of this is that it does
-not allow Jalview to dynamically request additional memory from the operating
-system. It is important, therefore, that you ensure that you have allocated
-enough memory to work with your data. On most occasions, Jalview will warn you
-when you have tried to load an alignment that is too big to fit in to memory (for
-instance, some of the PFAM alignments are {\bf very} large). You can find out how
-much memory is available to Jalview with the desktop window's {\sl $\Rightarrow$
-Tools $\Rightarrow$ Show Memory Usage} function, which enables the display of the
-currently available memory at the bottom left hand side of the Desktop window's
-background. Should you need to increase the amount of memory available to
-Jalview, full instructions are given in the built in documentation (opened by selecting {\sl Help $\Rightarrow$ Documentation})
-and on the JVM memory parameters page (http://www.jalview.org/jvmmemoryparams.html) on
-the website.
-
-
-\section{Writing sequence alignments}
-\label{savingalignments} \subsection{Saving the alignment} Jalview allows the
+Jalview is a Java program. One unfortunate implication of this is that Jalview
+cannot dynamically request additional memory from the operating system. It is
+important, therefore, that you ensure that you have allocated enough memory to
+work with your data. On most occasions, Jalview will warn you when you have
+tried to load an alignment that is too big to fit in to memory (for instance,
+some of the PFAM alignments are {\bf very} large). You can find out how much
+memory is available to Jalview with the desktop window's {\sl $\Rightarrow$
+Tools $\Rightarrow$ Show Memory Usage} function, which enables the display of
+the currently available memory at the bottom left hand side of the Desktop
+window's background. Should you need to increase the amount of memory available
+to Jalview, full instructions are given in the built in documentation (opened by
+selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory
+parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
+
+
+\section{Writing Sequence Alignments}
+\label{savingalignments} \subsection{Saving the Alignment} Jalview allows the
current sequence alignments to be saved to file so they can be restored at a
later date, passed to colleagues or analysed in other programs. From the
alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box
and format used to save (or load) the alignment, enabling you to quickly save
the file during or after editing by using the {\sl File $\Rightarrow$ Save} entry.
-Jalview offers several different formats in which an alignment can be saved. The jalview format (.jar) is the only one which will preserve the colours, groupings and similar information in the alignment. The other formats produce text files containing just the sequences with no visualization information, although some allow limited annotation and sequence features to be stored (e.g. AMSA). Unfortunately only Jalview can read Jalview files. The {\sl File $\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into other documents or web servers.
+Jalview offers several different formats in which an alignment can be saved. The
+jalview format (.jar) is the only format which will preserve the colours,
+groupings and other additional information in the alignment. The other formats
+produce text files containing just the sequences with no visualization information, although some
+allow limited annotation and sequence features to be stored (e.g. AMSA).
+Unfortunately only Jalview program can read Jalview files. The {\sl File
+$\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
+other documents or web servers.
%[fig 10]
\begin{figure}[htbp]
\parbox[c]{4in}{
\includegraphics[width=4in]{images/saveas2.pdf}
}
-\caption{{\bf Saving alignments in Jalview to disk}}
+\caption{{\bf Saving alignments in Jalview to disk.}}
\label{savealign}
\end{center}
\end{figure}
\subsection{Jalview Projects}
-\parbox[c]{4in}{If you wish to save the complete Jalview session rather than just one alignment (e.g. because you have calculated trees or multiple different alignments) then your work should be saved as a Jalview Project file\footnote{Tip: Ensure that you have allocated plenty of memory to Jalview when working with large alignments in Jalview projects. See Section \protect \ref{memorylimits} above for how to do this.}.
-From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save dialog box will appear. Loading a project will restore Jalview to exactly the view at which the file was saved, complete with all alignments, trees, annotation and displayed structures rendered appropriately.
-}
-\parbox[c]{2in}{
-\centerline {
-\includegraphics[width=1.5in]{images/saveproj.pdf}
-}}
+\parbox[c]{4in}{If you wish to save a complete Jalview session rather than
+just a single alignment (e.g. because you have calculated trees or multiple
+different alignments) then save your work as a Jalview Project
+file (.jvp).\footnote{Tip: Ensure that you have allocated plenty of memory to
+Jalview when working with large alignments in Jalview projects. See Section \protect
+\ref{memorylimits} above for how to do this.}
+From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save
+dialog box will appear. Loading a project will restore Jalview to exactly the
+view at which the file was saved, complete with all alignments, trees,
+annotation and displayed structures rendered appropriately.
+} \parbox[c]{2in}{ \centerline {
+\includegraphics[width=1.5in]{images/saveproj.pdf} }}
\exercise{Saving Alignments}{
\label{save}
-\exstep{Start Jalview, close all windows and load the ferredoxin alignment from
-PFAM (PFAM seed accession number PF03460 (see Exercise \ref{load}). }
-\exstep{
-Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a location into which to save the alignment and select a format. All formats except {\sl Jalview } can be viewed in a normal text editor (e.g. Notepad) or in a web browser. Enter a file name and click {\sl Save}. Check this file by closing all windows and opening it with Jalview or by
-browsing to it with your web browser.
-}
-\exstep{ Repeat the previous step trying different file formats.}
-\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}. You can select and copy this alignment to the clipboard using the textbox menu options {\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}. The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
-}
-\exstep{Ensure at least one alignment window is shown in Jalview. Open the
-overview window and scroll to any part of the alignment. Select {\sl File
-$\Rightarrow$ Save Project} from the main menu and save in a suitable place.
-Close all windows and then load the project {\sl via} the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } }
-
-
-\section{Selecting and editing sequences}
+\exstep{Launch Jalview, or use close all windows.
+Load the ferredoxin
+alignment from PFAM (seed) data base using the PFAM seed accession number
+PF03460 (see Exercise \ref{load}). } \exstep{
+
+Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
+location into which to save the alignment and select your prefered format. All
+formats except {\sl Jalview } jvp can be viewed in a normal text editor (e.g.
+Notepad) or in a web browser.
+Enter a file name and click {\sl Save}.
+
+Check this file by closing all windows and opening it with Jalview, or by
+browsing to it with your web browser.}
+\exstep{ Repeat the previous step saving the files in different file formats.}
+\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}.
+Select and copy this alignment to the clipboard using the textbox menu options
+{\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}.
+The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
+}
+\exstep{Ensure at least one alignment window is active in Jalview. Open the
+overview window {\sl View $\Rightarrow$ Overview Window}
+ and scroll red box to any part of the alignment.
+Select {\sl File
+$\Rightarrow$ Save Project} from the main menu and save the project in a
+suitable folder.
+
+Close all windows and then load the project {\sl via} the {\sl File
+$\Rightarrow$ Load Project} menu option. Observe how all the windows and
+positions are exactly as they were when they were saved. } }
+
+
+\section{Selecting and Editing Sequences}
\label{selectingandediting}
Jalview makes extensive use of selections - most of the commands available from
its menus operate on the {\sl currently selected region} of the alignment, either to
change their appearance or perform some kind of analysis. This section
illustrates how to make and use selections and groups.
-\subsection{Selecting parts of an alignment}
+\subsection{Selecting Parts of an Alignment}
Selections can be of arbitrary regions in an alignment, one or more complete columns, or one or more complete sequences.
A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ To New Alignment} in the alignment window menu options.
-To clear (unselect) the selection press the [ESC] (escape) key.
+{\bf To clear (unselect) the selection press the [ESC] (escape) key.}
-\subsubsection{Selecting arbitrary regions}
+\subsubsection{Selecting Arbitrary Regions}
To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button. A dashed red box appears around the selected region (Figure \ref{select}).
%[fig 12]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4in]{images/select1.pdf}
-\caption{{\bf Selecting a region in an alignment}}
+\caption{{\bf Selecting a region in an alignment.}}
\label{select}
\end{center}
\end{figure}
-\subsubsection{Selecting columns}
-To select the same residues in all sequences, click and drag along the alignment ruler. This selects the entire height of the alignment. Ranges of positions can also be selected by clicking on the first position then holding down the [SHIFT] key whilst clicking the other end of the selection. Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
+\subsubsection{Selecting Columns}
+To select the same residues in all sequences, click and drag along the alignment ruler.
+This selects the entire column of the alignment. Ranges of positions from the
+alignment ruler can also be selected by clicking on the first position and then
+holding down the [SHIFT] key whilst clicking the other end of the selection.
+Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
%[fig 13]
\begin{figure}[htbp]
\end{center}
\end{figure}
-\subsubsection{Selecting sequences}
+\subsubsection{Selecting Sequences}
\begin{figure}[htb]
\begin{center}
\end{figure}
To select multiple complete sequences, click and drag the mouse down the
-sequence ID panel. The same technique as used for columns above can be used with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous ranges of sequences (Figure \ref{selectrows}).
+sequence ID panel. The same techniques as used for columns (above) can be used
+with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous
+ranges of sequences (Figure \ref{selectrows}).
%[fig 14]
-\subsubsection{Making selections in Cursor mode}
+\subsubsection{Making Selections in Cursor Mode}
To define a selection in cursor mode (which is enabled by pressing [F2] when the alignment window is selected),
navigate to the top left corner of the proposed selection (using the mouse, the arrow keys, or the keystroke
\includegraphics[width=1.5in]{images/csel2.pdf}
\includegraphics[width=1.5in]{images/csel3.pdf}
\includegraphics[width=1.5in]{images/csel4.pdf}
-\caption{{\bf Making a selection in cursor mode.} Navigate to the top left corner (left), press [Q] (left center), navigate to the bottom right corner (right center) and press [M] (right)}
+\caption{{\bf Making a selection in cursor mode.} Navigate to the top left
+corner (left), press [Q] (left center), navigate to the bottom right corner (right center) and press [M] (right).}
\label{cselect}
\end{center}
\end{figure}
-\subsubsection{Inverting the current selection}
+\subsubsection{Inverting the Current Selection}
The current sequence or column selection can be inverted, using {\sl Select
$\Rightarrow$ Invert Sequence/Column Selection} in the alignment window.
visible, invert the selection, then select {\sl View $\Rightarrow$ Hide
$\Rightarrow$ Selected Region }.
-\subsection{Creating groups}
+\subsection{Creating Groups}
Selections are lost as soon as a different region is selected. Groups can be
created which are labeled regions of the alignment. To create a group, first
select the region which is to comprise the group. Then click the right mouse
\begin{center}
\includegraphics[width=3in]{images/group1.pdf}
\includegraphics[width=1.5in]{images/newgroup.pdf}
-\caption{{\bf Creating a new group from a selection}}
+\caption{{\bf Creating a new group from a selection.}}
\label{makegroup}
\end{center}
\end{figure}
By default the new group will have a box drawn around it. The appearance of the group can be changed (see Section \ref{colours} below). This group will stay defined even when the selection is removed.
-\subsection{Exporting the current selection}
+\subsection{Exporting the Current Selection}
-The current selection can be copied to the clipboard (in PFAM format). It can also be output to a textbox using the output functions in the pop-up menu obtained by right clicking the current selection. The textbox enables quick manual editing of the alignment prior to importing it into a new window (using the [New Window] button) or saving to a file with the {\sl File $\Rightarrow$ Save As } pulldown menu option from the text box.
+The current selection can be copied to the clipboard (in PFAM format). It can
+also be output to a textbox using the output functions in the pop-up menu
+obtained by right clicking the current selection. The textbox enables quick
+manual editing of the alignment prior to importing it into a new window (using
+the [New Window] button) or saving to a file with the {\sl File $\Rightarrow$
+Save As } pulldown menu option from the text box.
-\exercise{Making selections and groups}{
+\exercise{Making Selections and Groups}{
\label{exselect}
-\exstep{Close all windows in Jalview and load the ferredoxin alignment (PFAM
-ID PF03460). Choose a residue and place the mouse cursor on it. Click and drag the mouse cursor to create a selection. As you drag, a red box will `rubber band' out to show the extent of the selection. Release the mouse button and a red box should border the selected region. Now press [ESC] to clear the selection.} \exstep{
-Select one sequence by clicking on the ID panel. Note that the sequence ID takes on a highlighted background and a red box appears around the selected sequence. Now hold down [SHIFT] and click another sequence ID a few positions above or below. Note how the selection expands to include all the sequences between the two positions on which you clicked.
-Now hold down [CTRL] and click on several sequences ID's both selected and unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are individually deselected.
-}
-\exstep{ Repeat the step above but selecting columns by clicking on the ruler bar instead of selecting rows by clicking on the sequence ID.
-}
-\exstep{Press [F2] to enter Cursor mode. Navigate to column 59, row 1 by pressing {\sl 5 9 , 1 [RETURN]}. Press {\sl Q} to mark this position. Now navigate to column 65, row 8 by pressing {\sl 6 5 , 8 [RETURN]}. Press {\sl M} to complete the selection.}
-\exstep{\label{exselectgrpcolour}Open the popup menu by right-clicking the
-selected region with the mouse. Open the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour } menu and select `Percentage Identity'. This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences by clicking on their Sequence ID label. Note how the group expands to include newly selected sequences, and the `Percentage Identity' colouring changes. }
-\exstep{
-Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
-
-\exstep{
-Right click on the text area to open the selection popup-menu. Follow the menus and pick an output format from the {\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
-}
-\exstep{Try manually editing the alignment and then press the [New Window] button to import the file into a new alignment window.}
+\exstep{Close all windows in Jalview.
+Load the ferredoxin alignment (PFAM
+ID PF03460 from PFAM seed database).
+Choose a residue and place the mouse
+cursor on it. Note residue information will show in alignment window status bar.
+Click and drag the mouse cursor to create a selection. As you drag, a red box
+will `rubber band' out to
+show the extent of the selection.
+Release the mouse
+button and a red box should border the selected region.
+Press [ESC] to clear the selection.}
+\exstep{ Select one sequence by clicking on
+the sequence ID panel. Note that the sequence ID takes on a highlighted
+background and a red box appears around the selected sequence.
+Hold down [SHIFT] and click another sequence ID a few positions above or below.
+Note how the selection expands to include all the sequences between the two positions on which you clicked.
+
+Hold down [CTRL] and then click on several sequences ID's both selected and
+unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are
+individually deselected.}
+\exstep{ Select column by clicking on the Alignment Ruler. Note whole
+column is highlighted with a red box.
+Hold down [SHIFT] and click column beyond. Note the selection expands to include
+all the sequences between the two positions on which you clicked.}
+
+\exstep{ To selecting arbitrary regions in alignment, place the mouse at the top
+left corner of the region you wish to select. Press and hold the mouse button.
+Drag the mouse to the bottom right corner of the chosen region and release the
+mouse button and a dashed red box appears around the selected region}
+\exstep{Enter Cursor mode using [F2] (or [Fn]-F2 for Macs).
+Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
+Press {\bf Q} to mark this position.
+Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
+to complete the selection. Note to clear the selection press the {\bf[ESC]}
+key.} \exstep{To create a {\bf group} from the selected the region, click the
+right mouse button when mouse is on the selection, this opens the selection
+popup menu in the alignment window.
+
+Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
+} menu and select `Percentage Identity'.
+This will turn the selected region into a group and colour it accordingly.}
+\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
+the alignment by clicking on their Sequence ID label. Note how the group expands
+to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
+
+\exstep{The current selection can be {\bf exported} and saved by right clicking
+on the text area to open the selection popup-menu. Follow the menus and pick an
+output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
+\ldots} submenu.
+}
+\exstep{In the alignment output window, try manually editing the alignment,
+importing group into a new alignment window by clicking the [New Window] button to import the
+file into a new alignment window.}
% more? change colouring style. set border colour.
}
-\subsection{Reordering the alignment}
+\subsection{Reordering the Alignment}
Sequence reordering is simple. Highlight the sequences to be moved then press the up or down arrow keys as appropriate (Figure \ref{reorder}). If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and then move the group rather than the individual sequence.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=3in]{images/move1.pdf}
\includegraphics[width=3in]{images/move2.pdf}
-\caption{{\bf Reordering the alignment.} The selected sequence moves up one position on pressing the $\uparrow$ key}
+\caption{{\bf Reordering the alignment.} The selected sequence moves up one
+position on pressing the $\uparrow$ key.}
\label{reorder}
\end{center}
\end{figure}
-\exercise{Reordering the alignment}{
-\exstep{Open an alignment (e.g.the PFAM domain PF03460). Select one sequence. Using the up and down arrow keys, alter its position in the alignment. Note that this will not work in cursor mode.
-}
-\exstep{Hold [CTRL] and select two sequences separated by one or more un-selected sequences. Note how multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.
-}
-}
+\exercise{Reordering the Alignment}{
+\exstep{Close all windows in Jalview from desktop. Load the ferredoxin alignment (e.g.the
+PFAM domain PF03460 from PFAM seed).
+Select one of the sequence in the sequence ID panel, use the up and down
+arrow keys to alter the sequence's position in the alignment. (Note that
+this will not work in cursor mode)}
+\exstep{To select and move multiple
+sequences, use hold [SHIFT] and [CTRL], and select two sequences separated by
+one or more un-selected sequences. Note how multiple sequences are grouped
+together when they are re-ordered using the up and down arrow keys.} }
-\subsection{Hiding regions}
+\subsection{Hiding Regions}
\label{hidingregions}
It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create the several different views in the example alignment file that is loaded when Jalview is first started (See Figure \ref{startpage}).
-To hide a set of sequences, select them and right-click the mouse on the selected sequence IDs to bring up the context menu. Select {\sl Hide Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
+To hide a set of sequences, select them and right-click the mouse on the
+selected sequence IDs to bring up the context pop-up menu. Select {\sl Hide
+Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
\begin{figure}[htbp]
\includegraphics[width=1.5in]{images/hide1.pdf}
\includegraphics[width=2.5in]{images/hide2.pdf}
\includegraphics[width=1.75in]{images/hide3.pdf}
-\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small blue triangle in the sequence ID panel}
+\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small blue
+triangle in the sequence ID panel.}
\label{hideseq}
\end{center}
\end{figure}
-A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns (indicated by a red marker) can be hidden and revealed in the same way {\sl via} the context menu by right clicking on the ruler bar. The hidden column selection is indicated by a small blue triangle in the ruler bar.
+A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns
+(indicated by a red marker) can be hidden and revealed in the same way {\sl via}
+the context pop-up menu by right clicking on the ruler bar. The hidden column
+selection is indicated by a small blue triangle in the ruler bar.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2in]{images/hide4.pdf}
\includegraphics[width=3in]{images/hide5.pdf}
\includegraphics[width=1in]{images/hide6.pdf}
-\caption{{\bf Hiding Columns} Hidden columns are represented by a small blue triangle in the ruler bar}
+\caption{{\bf Hiding Columns} Hidden columns are represented by a small blue
+triangle in the ruler bar.}
\label{hidecol}
\end{center}
\end{figure}
$\Rightarrow$ All but Selected Region } menu entry, or press [Shift]+[Ctrl]+H
to hide the unselected region.
-\subsubsection{Representing a group with a single sequence}
+\subsubsection{Representing a Group with a Single Sequence}
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
\exercise{Hiding and revealing regions}{
-\exstep{Close all windows then open the PFAM accession PF03460. Select a contiguous set of sequences by clicking and dragging on the sequence ID panel. Right click on the selected sequence IDs and select {\sl Hide Sequences}.
+\exstep{Close all windows, open the PFAM accession PF03460. Select a
+contiguous set of sequences by clicking and dragging on the sequence ID panel.
+Right click on the selected sequence IDs to bring up the selection pop-up menu, select {\sl Hide Sequences}.
}
\exstep{
-Right click on the blue triangle indicating hidden sequences and select {\sl Reveal Sequences}. (If you have hidden all sequences then you will need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.})
-}
+Right click on the blue triangle indicating hidden sequences and select {\sl
+Reveal Sequences} in the panel. (If you have hidden all sequences then you will
+need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.}) }
\exstep{
-Repeat but using a non-contiguous set of sequences. Note that when multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
+Repeat the process but use a non-contiguous set of sequences. Note that when
+multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
}
-\exstep{Repeat the above but hiding and revealing columns instead of sequences.
-}
-\exstep{Select a region of the alignment, add in some additional columns to the
-selection, and experiment with the `Hide all but selected region' function. }
-\exstep{Select some sequences and pick one to represent the rest. Bring up the sequence ID pop-up menu for that sequence and select the {\sl Represent group with $<$Sequence ID$>$ } option. Use the pop-up menu again to reveal the hidden sequences that you just picked a representative for.}
+\exstep{Repeat the above using columns to hide and reveale columns
+instead of sequences.
}
+\exstep{Select a region of the alignment, then add in some additional columns to
+the selection, and experiment with the `Hide all but selected region' function
+in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
+\exstep{Select some sequences and pick one to represent the rest by hoovering
+the mouse over this sequence. Bring up the selection pop-up menu by right
+clicking and then seelct {\sl (Sequence ID) $\Rightarrow$ Represent group
+with (Sequence ID)}. To reveal these hidden sequences, right click on the
+Sequence ID and in the the pop-up menu select Reveal All.}}
-\subsection{Introducing and removing gaps}
+\subsection{Introducing and Removing Gaps}
The alignment view provides an interactive editing interface, allowing gaps to be inserted or deleted to the left of any position in a sequence or sequence group. Alignment editing can only be performed whilst in keyboard editing mode (entered by pressing [F2]) or by clicking and dragging residues with the mouse when [SHIFT] or [CTRL] is held down (which differs from earlier versions of Jalview).
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 $\Rightarrow$
+ \item{Remember to use [CTRL]+Z to undo an edit, or the {\sl 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
}
\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
+on the sequence IDs to open the sequence ID popup menu, and select {\sl Hide
Sequences}). }
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
\subsubsection{Editing in Cursor mode}
-Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE] or [SHIFT]-[SPACE] (both keys held down together).
-
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you have everything unselected by pressing ESC. The gap under the cursor will be removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps will be deleted up to the number specified. To delete gaps from all sequences of a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down together). Note that the deletion will only occur if the gaps are in the same columns in all sequences in the selected group, and those columns are to the right of the selected residue.
-
-\exercise{Keyboard edits}{
-\item{This continues on from exercise \ref{mousealedit}, and recreates the final
-part of the example ferredoxin alignment from the unaligned sequences using
-Jalview's keyboard editing mode. Note that using the [SHIFT]-[SPACE] command should have the same effect as the [CTRL]-[SPACE] command mentioned in this exercise.}
-
-\exstep{Load the
-sequence alignment at \textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the edited alignment from exercise \ref{mousealedit}. If you continue from the previous exercise, then first right click on the sequence ID panel and select {\tr Reveal All}.
+Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by
+pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
+under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
+press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
+or [SHIFT]-[SPACE] (both keys held down together).
+
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
+have everything unselected by pressing ESC. The gap under the cursor will be
+removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
+will be deleted up to the number specified. To delete gaps from all sequences of
+a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
+together). Note that the deletion will only occur if the gaps are in the same
+columns in all sequences in the selected group, and those columns are to the
+right of the selected residue.
+
+\exercise{Keyboard edits}{ \item{This continues on from exercise
+\ref{mousealedit}, and recreates the final part of the example ferredoxin
+alignment from the unaligned sequences using Jalview's keyboard editing mode.
+
+{\bf {\sl Note for Windows Users:}} The [SHIFT]-[SPACE] command has the same effect as
+the [CTRL]-[SPACE] command mentioned in this exercise, and you should use
+[SHIFT]-[SPACE] in order to avoid opening the window menu.}
+
+\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
+{\sl Reveal All}.
Now, enter cursor mode by pressing [F2]}
-%TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
+% TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
\exstep{Insert 58 gaps at the start of the first sequence (FER\_CAPAA). Press {\sl 58} then {\sl [SPACE]}. }
\exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN). Hold down shift and click on the fifth (FER1\_PEA). }
\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing {\sl 1,2} then pressing {\sl [RETURN]}. Now insert 6 gaps. Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.}
-\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47. Press {\sl 34C} then
-{\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE]. Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are now aligned.}
+\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
+Press {\sl 34C} then {\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE].
+Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are
+now aligned.}
\exstep{The fifth sequence (FER1\_PEA) is poorly aligned. We will delete some gaps and add some new ones. Press {\sl [ESC]} to clear the selection. Navigate to the start of sequence 5 and delete 3 gaps. Press {\sl 1,5 [RETURN]} then {\sl 3 [BACKSPACE]} to delete three gaps. Go to column 31 and delete the gap. Press {\sl 31C [BACKSPACE]} .}
\exstep{ Similarly delete the gap now at column 34, then insert two gaps at column 38. Press {\sl 34C [BACKSPACE] 38C 2 [SPACE]}. Delete three gaps at column 44 and insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are now aligned.}
}
-\section{Colouring sequences}
+\section{Colouring Sequences}
\label{colours}
Colouring sequences is a key aspect of alignment presentation. Jalview allows
There are two main types of colouring styles: simple static residue colourschemes and dynamic schemes which use conservation and consensus analysis to control colouring. A hybrid colouring is also possible, where static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
-\subsection{Colouring the whole alignment}
+\subsection{Colouring the Whole Alignment}
\parbox[c]{3.75in}{The alignment can be coloured {\sl via} the {\sl Colour} menu option in the alignment window. Selecting the colour scheme causes all residues to be coloured. The menu is divided into three sections. The first section gives options for the behaviour of the menu options, the second lists static and dynamic colourschemes available for selection. The last gives options for making hybrid colourschemes using conservation shading or colourscheme thresholding.
}
}
-\subsection{Colouring a group or selection}
+\subsection{Colouring a Group or Selection}
Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above, after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected. This must be turned {\sl off} specifically as it is {\sl on} by default. When unticked, selections from the Colours menu will only change the colour for residues in the current selection, or the alignment view's ''background colourscheme'' when no selection exists.
\end{center}
\end{figure}
-\subsection{Shading by conservation}
+\subsection{Shading by Conservation}
For many colour schemes, the intensity of the colour in a column can be scaled
by the degree of amino acid property conservation. Selecting {\sl Colour
$\Rightarrow$ By Conservation} enables this mode, and {\sl Modify
\end{center}
\end{figure}
-\subsection{Thresholding by percentage identity}
+\subsection{Thresholding by Percentage Identity}
`Thresholding' is another hybrid colour model where a residue is only coloured
if it is not excluded by an applied threshold. Selecting {\sl Colour $\Rightarrow$ Above Identity Threshold} brings up a selection box with a slider controlling the minimum percentage identity threshold to be applied. Selecting a higher threshold (by sliding to the right) limits the colouring to columns with a higher percentage identity (as shown by the Consensus histogram in the annotation panel).
\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
+\parbox[c]{3.2in}{
+Any of the {\bf 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} option 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).
+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}
+Default settings for minimum and maximum colours can be set in the Jalview
+Desktop's preferences.
+}\parbox[c]{3in}{
+\centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
+
+The {\bf per Sequency only} option in the {\bf Colour By Annotation} dialog
+allows each sequence to be shaded according to sequence associated annotation
+rows, such as protein disorder scores. This functionality is described futher in
+Section \ref{protdisorderpred}.
+
+\subsection{Colour Schemes}
\label{colscheme}
Full details on each colour scheme can be found in the Jalview on-line help. A brief description of each one is provided below:
\subsubsection{Percentage Identity}
\parbox[c]{3.5in}{
-The Percent Identity option colours the residues (boxes and/or text) according to the percentage of the residues in each column that agree with the consensus sequence. Only the residues that agree with the consensus residue for each column are coloured.
+The Percent Identity option colours the residues (boxes and/or text) according to the percentage of the residues in each column that agree with the consensus sequence. Only the residues that agree with the consensus residue for each column are coloured.
}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_percent.pdf}
\subsubsection{Nucleotide}
-\parbox[c]{3.5in}{
-Residues are coloured with four colours corresponding to the four nucleotide bases. All non ACTG residues are uncoloured. See Section \ref{workingwithnuc} for further information about working with nucleic acid sequences and alignments.
-}
-\parbox[c]{3in}{
-\includegraphics[width=2.75in]{images/col_nuc.pdf}
-}
-
-
+\parbox[c]{3.5in}{ Residues are coloured with four colours corresponding to the
+four nucleotide bases. All non ACTG residues are uncoloured. See Section
+\ref{workingwithnuc} for further information about working with nucleic acid
+sequences and alignments.
+} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_nuc.pdf} }
+
+\subsubsection{Purine Pyrimidine}
+\parbox[c]{3.5in}{ Residues are coloured according to whether the corresponding
+nucleotide bases are purine (magenta) or pyrimidine (cyan) based. All non ACTG
+residues are uncoloured. For further information about working with nucleic acid
+sequences and alignments, see Section \ref{workingwithnuc}
+%and Section \ref{workingwithrna}
+.
+
+} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_purpyr.pdf} }
+
+\subsubsection{RNA Helix colouring}
+\parbox[c]{3.5in}{ Columns are coloured according to their assigned RNA helix as
+defined by a secondary structure annotation line on the alignment. Colours for
+each helix are randomly assigned, and option only available when an RNA
+secondary structure row is present on the alignment.
+% For more details see Section \ref{workingwithrna}
+} \parbox[c]{3in}{
+\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
\exercise{Colouring Alignments}{
\exstep{
Open a sequence alignment, for example the PFAM domain PF03460. Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
}
\exstep{
-Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in the group selection exercise step \ref{exselectgrpcolour}).
+Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in exercise \ref{exselectgrpcolour} during the group selection step).
}
\exstep{
Keeping the same selection as before, colour the complete alignment using {\sl Colour $\Rightarrow$ Taylor}. Select the menu option {\sl Colour $\Rightarrow$ By Conservation}. Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
}
}
-\section{Alignment formatting and graphics output}
+\section{Alignment Formatting and Graphics Output}
\label{layoutandoutput}
Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output, the layout that is seen on screen will be the same as what is output in an exported graphics file. It is therefore important to pick the right kind of display layout prior to generating figures.
\subsection{Multiple Alignment Views}
-Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\tr Views}. Because each view displays the same underlying data, any edits performed in one view will update the alignment or annotation visible in all views.
+Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\sl Views}. Because each view displays the same underlying data, any edits performed in one view will update the alignment or annotation visible in all views.
\parbox[c]{4in}{Alignment views are created using the {\sl View $\Rightarrow$ New View} option of the alignment window or by Pressing [CTRL]-T. This will create a new view with the same groups, alignment layout and display options as the current one. Pressing G will gather together Views as named tabs on the alignment window, and pressing X will expand gathered Views so they can be viewed simultaneously in their own separate windows. To delete a group, press [CTRL]-W.}\parbox[c]{2.75in}{
\begin{center}\centerline{
% JBPNote make an excercise on views ?
-\subsection{Alignment layout}
+\subsection{Alignment Layout}
Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped, where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
\subsubsection{Wrapped alignments}
\begin{center}
\parbox[c]{2in}{\includegraphics[width=2in]{images/wrap1.pdf}}
\parbox[c]{4in}{\includegraphics[width=4in]{images/wrap2.pdf}}
-\caption{{\bf Wrapping the alignment}}
+\caption{{\bf Wrapping the alignment.}}
\label{wrap}
\end{center}
\end{figure}
display gaps or sequence symbols that differ from the consensus for each
column, and render all others with a `.'.
%TODO add a graphic to illustrate this.
-\subsection{Annotation ordering and display}
+\subsection{Annotation Ordering and Display}
% TODO: describe consensus, conservation, quality user preferences, and group
% annotation preferences.
The annotation lines which appear below the sequence alignment are described in
\begin{center}
\includegraphics[width=2.5in]{images/annot1.pdf}
\includegraphics[width=2.5in]{images/annot2.pdf}
-\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl View} menu (left) or individually from the context menu (right)}
+\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl
+View} menu (left) or individually from the context menu (right).}
\label{annot}
\end{center}
\end{figure}
\label{exscreen}
\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}. Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. Experiment with the various options from the {\sl Format} menu. to adjust the ruler placement, sequence ID format and so on. }
\exstep{Hide all the annotation rows by selecting {\sl View $\Rightarrow$ Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.}
-\exstep{Right click on the annotation row labels to bring up the context menu. Select {\sl Hide This Row}. Bring up the context menu again and select {\sl Show All Hidden Rows} to reveal them}
+\exstep{{\bf Deselect} {\sl Format $\Rightarrow$ Wrap}, and right click on the annotation row labels to bring up the context menu. Select {\sl Hide This Row}. Bring up the context menu again and select {\sl Show All Hidden Rows} to reveal them}
\exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot} below.}
\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label - a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed by Clicking and dragging the mouse up or down.}
}
-\subsection{Graphical output}
+\subsection{Graphical Output}
\label{figuregen}
\parbox[c]{4in}{Jalview allows alignments figures to be exported in three different formats, each of which is suited to a particular purpose. Image export is {\sl via} the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ \ldots } alignment window menu option. }
\parbox[c]{2in}{\centerline{\includegraphics[width=1.25in]{images/image.pdf}}}
\label{analysisannotation}
This chapter describes the annotation, analysis, and visualization tasks that
-the Jalview Desktop can perform. Section \ref{wkwithstructure} introduces the
-structure visualization capabilities of Jalview. In Section \ref{alignanalysis},
-you will find details of the Tree building, viewing and PCA capabilities,
+the Jalview Desktop can perform.
+
+Section \ref{wkwithstructure} introduces the structure visualization
+capabilities of Jalview. In Section \ref{alignanalysis}, you will find
+descriptions and exercises on building and displaying trees, PCA analysis,
alignment redundancy removal, pairwise alignments and alignment conservation
analysis. Section \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Section \ref{msaservices}
-describes how to use the range of multiple alignment programs provided by JABA
-(see Section \ref{jabaservices}). Similarly, Section \ref{protsspredservices}
-explains how to perform protein secondary structure predictions with JPred.
-
-Section \ref{featannot} describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation and how they are displayed, imported and exported. Section \ref{featuresfromdb} discusses the retrieval of database references and establishment of sequence coordinate systems for the retrieval and display of features from databases and DAS annotation services. Finally, Section \ref{workingwithnuc} describes functions and visualization techniques relevant to working with nucleotide sequences, coding region annotation and nucleotide sequence alignments.
+available to Jalview users, and Section \ref{jabaservices} explains how to
+configure the Jalview Desktop for access to new JABAWS servers.
+Section \ref{msaservices} describes how to use the range of multiple alignment
+programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS' AACon
+service for protein multiple alignment conservation analysis.
+Section \ref{protsspredservices} explains how to perform protein secondary
+structure predictions with JPred, and JABAWS' protein disorder prediction
+services are introduced in Section \ref{protdisorderpred}.
+
+Section \ref{featannot} describes the mechanisms provided by Jalview for
+interactive creation of sequence and alignment annotation, and how they can be
+displayed, imported and exported and used to reorder the alignment. Section
+\ref{featuresfromdb} discusses the retrieval of database references and
+establishment of sequence coordinate systems for the retrieval and display of
+features from databases and DAS annotation services. Section
+\ref{workingwithnuc} describes functions and visualization techniques relevant
+to working with nucleotide sequences, coding region annotation and nucleotide
+sequence alignments.
+% and Section \ref{workingwithrna} covers the visualization,
+% editing and analysis of RNA secondary structure.
\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.
+Jalview facilitates the use of protein structures for the analysis of alignments
+by providing a linked view of structures associated with 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 European Protein Databank (PDBe) using the Sequence Fetcher (see
\ref{fetchseq}).
structures. This takes a few seconds and applies to all sequences in the
alignment which have valid Uniprot IDs. On moving the cursor over the sequence
ID the tool tip\footnote{Tip: The sequence ID tooltip can often become large for
-heavily cross referenced sequence IDs. Use the {\sl View $\Rightarow$ Sequence
+heavily cross referenced sequence IDs. Use the {\sl View $\Rightarrow$ Sequence
ID Tooltip $\Rightarrow$ } submenu to disable the display of database cross
references or non-positional features. } now shows the Uniprot ID and any
associated PDB structures.
\subsubsection{Drag-and-drop association of PDB files with sequences by filename
match}
\label{multipdbfileassoc}
-If one or more PDB files stored on your computer are dragged from their location on the file browser
-onto an alignment window, Jalview will search the alignment for sequences with IDs that
-match any of the files dropped onto the alignment. If it discovers matches, a
-dialog like the one in Figure \ref{multipdbfileassocfig} is shown, giving the
-option of creating associations for the matches.
+If one or more PDB files stored on your computer are dragged from their location
+on the file browser onto an alignment window, Jalview will search the alignment
+for sequences with IDs that match any of the files dropped onto the alignment.
+If it discovers matches, a dialog like the one in Figure
+\ref{multipdbfileassocfig} is shown, giving the option of creating associations
+for the matches.
If no associations are made, then sequences extracted
from the structure will be simply added to the alignment. However, if only
\includegraphics[]{images/pdbdragdropassoc.pdf}
\caption{{\bf Associating PDB files with sequences by drag-and-drop.} Dragging
-PDB files onto an alignment of sequences with names matching the dragged
-files names (A), results in a dialog box (B) that gives the option to associate each file with any sequences with matching IDs. }
+PDB files onto an alignment of sequences with names matching the dragged files
+names (A), results in a dialog box (B) that gives the option to associate each
+file with any sequences with matching IDs. }
\label{multipdbfileassocfig}
\end{center}
\end{figure}
-\subsection{Viewing Protein Structures}
+\subsection{Viewing Structures}
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}
+a set of sequences in an alignment. If any of the {\bf 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}
+sequence ID popup menu will include an option to {\sl View {\bf N}
structures}. Selecting this option will open a new structure view containing
the associated structures superposed according to the alignment.
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 or by [SHIFT]-dragging the structure.
+window. The structure can be zoomed using the mouse scroll wheel or by
+[SHIFT]-dragging the structure.
Moving the mouse cursor over a sequence to which the structure is linked in the
alignment view highlights the respective residue's sidechain atoms. The
sidechain highlight may be obscured by other parts of the molecule. Similarly,
moving the cursor over the structure shows a tooltip and highlights the
-corresponding residue in the alignment. Clicking the alpha carbon toggles the highlight
-and residue label on and off. Often, the position highlighted in the sequence may not
-be in the visible portion of the current alignment view. If the alignment
-window's {\sl View $\Rightarrow$ Automatic Scrolling } option is selected, however,
-then Jalview will automatically move the alignment scroll bars to show the
-highlighted region.
+corresponding residue in the alignment. Clicking the alpha carbon or phosphorous
+backbone atom will toggle the highlight and residue label on and off. Often, the
+position highlighted in the sequence may not be in the visible portion of the
+current alignment view and the sliders will scroll automatically to show the
+position. If the alignment window's {\sl View $\Rightarrow$ Automatic Scrolling
+} option is not selected, however, then the automatic adjustment will be
+disabled for the current view.
\begin{figure}[htbp]
\begin{center}
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
-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 saved as an EPS or PNG with the {\sl File $\Rightarrow$ Save As
-$\Rightarrow$ \ldots} submenu, which also allows the raw data to be saved as PDB format. The mapping between the structure and the
-sequence (How well and which parts of the structure relate to the sequence)
-can be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
+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 saved as an EPS or PNG with the {\sl File
+$\Rightarrow$ Save As $\Rightarrow$ \ldots} submenu, which also allows the raw
+data to be saved as PDB format. The mapping between the structure and the
+sequence (How well and which parts of the structure relate to the sequence) can
+be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
\subsubsection{Using the Jmol visualization interface }
Jmol has a comprehensive set of selection and visualization functions that are
accessed from the Jmol popup menu (by right-clicking in the Jmol window or by
-clicking the Jmol logo). Molecule colour and rendering style can be
-manipulated, and distance measurements and molecular surfaces can be added to
-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}
+clicking the Jmol logo). Molecule colour and rendering style can be manipulated,
+and distance measurements and molecular surfaces can be added to the view. It
+also has its own ``Rasmol\footnote{See \url{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.
+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
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}.
+the alignment.
+% JBP Note: Bug JAL-1238 needs to be fixed ASAP
+
+{\bf Note:} If you are using Jalview v2.8 - use the {\sl Uniprot } source from the {\sl Web services $\Rightarrow$ Fetch DB References $\Rightarrow$ ..} submenu of the Alignment Window to retrieve the PDB IDs. }
+\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 OK to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with a suitable program. }
\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
+biochemical properties of a given molecule are significantly 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
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}
+\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
structures.
\subsubsection{Obtaining the RMSD for a superposition}
-The RMSD (Root Mean Square Deviation) is a measure of how similar the structures are when they are superimposed. Figure \ref{mstrucsuperposition} shows a superposition created during the course
-of Exercise \ref{superpositionex}. The 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.
+The RMSD (Root Mean Square Deviation) is a measure of how similar the structures
+are when they are superimposed. Figure \ref{mstrucsuperposition} shows a
+superposition created during the course of Exercise \ref{superpositionex}. The
+parts of each molecule used to construct the superposition are rendered using
+the cartoon style, with other parts of the molecule drawn in wireframe. The Jmol
+console, which has been opened after the superposition was performed, shows the
+RMSD report for the superposition.
+Full information about the superposition is also output to the Jalview
+console.\footnote{The Jalview Java Console is opened from {\sl Tools
+$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
+includes the precise atom pairs used to superpose structures.
\subsubsection{Choosing which part of the alignment is used for structural
-superposition}
-Jalview uses the visible part of each alignment view to define which parts of
-each molecule are to be superimposed. Hiding a column in a view used for
-superposition will remove that correspondence from the set, and will exclude it from the superposition and RMSD calculation.
+superposition} Jalview uses the visible part of each alignment view to define
+which parts of each molecule are to be superimposed. Hiding a column in a view
+used for superposition will remove that correspondence from the set, and will
+exclude it from the superposition and RMSD calculation.
This allows the selection of specific parts of the alignment to be used for
superposition. Only columns that define a complete set of correspondences for
all structures will be used for structural superposition, and as a consequence,
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. }
+after the superposition is shown in the Jmol console.}
\label{mstrucsuperposition}
\end{center}
\end{figure}
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.}}
+moved on to the other. If this doesn't happen, use the Align function in the Jmol submenu}}
\exstep{Create a new view on the alignment, and hide all but columns 121
through to 132.}
\exstep{Use the {\sl Jmol} submenu to
\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
+\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. This
is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA server.}
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
{\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.}
+{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
\exstep{Drag the structure you downloaded in
step 1 onto one of the alignments to associate it with the mouse sequence in
that Pfam domain family.}
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
\section{Analysis of alignments}
\label{alignanalysis}
-Jalview provides support for sequence analysis in two ways. A number of analytical methods are `built-in', these are accessed from the {\sl Calculate} alignment window menu. Computationally intensive analyses are run outside Jalview {\sl via} web services - these are typically accessed {\sl via} the {\sl Web Service} menu, and described in \ref{jvwebservices} and subsequent sections. In this section, we describe the built-in analysis capabilities common to both the Jalview Desktop and the JalviewLite applet.
+Jalview provides support for sequence analysis in two ways. A number of
+analytical methods are `built-in', these are accessed from the {\sl Calculate}
+alignment window menu. Computationally intensive analyses are run outside
+Jalview {\sl via} web services - these are typically accessed {\sl via} the {\sl
+Web Service} menu, and described in \ref{jvwebservices} and subsequent sections.
+In this section, we describe the built-in analysis capabilities common to both
+the Jalview Desktop and the JalviewLite applet.
\subsection{PCA}
-This calculation creates a spatial representation of the similarities within the current selection or the whole alignment if no selection has been made. After the calculation finishes, a 3D viewer displays the each sequence as a point in 3D `similarity space'. Sets of similar sequences tend to lie near each other in this space.
-Note: The calculation is computationally expensive, and may fail for very large sets of sequences - because the JVM has run out of memory. Memory issues, and how to overcome them, were discussed in Section \ref{memorylimits}.
-\subsubsection{What is PCA?}
+This calculation creates a spatial representation of the similarities within the
+current selection or the whole alignment if no selection has been made. After
+the calculation finishes, a 3D viewer displays the each sequence as a point in
+3D `similarity space'. Sets of similar sequences tend to lie near each other in
+this space.
+Note: The calculation is computationally expensive, and may fail for very large
+sets of sequences - because the JVM has run out of memory. Memory issues, and
+how to overcome them, were discussed in Section \ref{memorylimits}.
-Principal components analysis is a technique for examining the structure of complex data sets. The components are a set of dimensions formed from the measured values in the data set, and the principle component is the one with the greatest magnitude, or length. The sets of measurements that differ the most should lie at either end of this principle axis, and the other axes correspond to less extreme patterns of variation in the data set.
-In this case, the components are generated by an eigenvector decomposition of the matrix formed from the sum of BLOSUM scores at each aligned position between each pair of sequences. The basic method is described in the 1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl Nature Structural Biology} (1995) {\bf 2}, 171-8.
+\subsubsection{What is PCA?}
+Principal components analysis is a technique for examining the structure of
+complex data sets. The components are a set of dimensions formed from the
+measured values in the data set, and the principle component is the one with the
+greatest magnitude, or length. The sets of measurements that differ the most
+should lie at either end of this principle axis, and the other axes correspond
+to less extreme patterns of variation in the data set.
+In this case, the components are generated by an eigenvector decomposition of
+the matrix formed from the sum of pairwise substitution scores at each aligned
+position between each pair of sequences. The basic method is described in the
+1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl
+Nature Structural Biology} (1995) {\bf 2}, 171-8.
PMID: 7749921} and implemented at the SeqSpace server at the EBI.
+Jalview provides two different options for the PCA calculation. Protein PCAs are
+by default computed using BLOSUM 62 pairwise substitution scores, and nucleic
+acid alignment PCAs are computed using a score model based on the identity
+matrix that also treats Us and Ts as identical, to support analysis of both RNA
+and DNA alignments. The {\sl Change Parameters} menu also allows the calculation
+method to be toggled between SeqSpace and a variant calculation that is detailed
+in Jalview's built in documentation.\footnote{See
+\url{http://www.jalview.org/help/html/calculations/pca.html}.}
+
\subsubsection{The PCA Viewer}
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle Component Analysis} menu option. {\bf PCA requires a selection containing at least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}). Each sequence is represented by a small square, coloured by the background colour of the sequence ID label. The axes can be rotated by clicking and dragging the left mouse button and zoomed using the $\uparrow$ and $\downarrow$ keys or the scroll wheel of the mouse (if available). A tool tip appears if the cursor is placed over a sequence. Sequences can be selected by clicking on them. [CTRL]-Click can be used to select multiple sequences.
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle
+Component Analysis} menu option. {\bf PCA requires a selection containing at
+least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}).
+Each sequence is represented by a small square, coloured by the background
+colour of the sequence ID label. The axes can be rotated by clicking and
+dragging the left mouse button and zoomed using the $\uparrow$ and $\downarrow$
+keys or the scroll wheel of the mouse (if available). A tool tip appears if the
+cursor is placed over a sequence. Sequences can be selected by clicking on them.
+[CTRL]-Click can be used to select multiple sequences.
\begin{figure}[hbtp]
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\label{PCA}
\end{center}
\end{figure}
-Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$ Show Labels} menu option, and the plot background colour changed {\sl via} the {\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical representation of the PCA plot can be exported as an EPS or PNG image {\sl via} the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
-\exercise{Principle Component Analysis}{
-\exstep{Load the alignment at
+Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$
+Show Labels} menu option, and the plot background colour changed {\sl via} the
+{\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical
+representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
+the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
+
+\exercise{Principle Component Analysis}{ \exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar} and press [ESC] to clear any selections. Alternatively, select {\sl Select $\Rightarrow$ Undefine Groups} to remove all groups and colourschemes. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
-\exstep{
-Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups, each of a different colour. Note how the colour of the sequence ID label matches both the colour of the partitioned tree and the points in the PCA plot.
-}
-}
+\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.
+} }
+
+\subsubsection{PCA data export}
+Although the PCA viewer supports export of the current view, the plots produced
+are rarely suitable for direct publication. The PCA viewer's {\sl File} menu
+includes a number of options for exporting the PCA matrix and transformed points
+as comma separated value (CSV) files. These files can be imported by tools such
+as {\bf R} or {\bf gnuplot} in order to graph the data.
\subsection{Trees}
\label{trees}
-Jalview can calculate and display trees, providing interactive tree-based grouping of sequences though a tree viewer. All trees are calculated {\sl via} the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu. Trees can be calculated from distance matrices determined from \% identity or aggregate BLOSUM 62 score using either {\sl Average Distance} (UPGMA) or {\sl Neighbour Joining} algorithms. The input data for a tree is either the selected region or the whole alignment, excluding any hidden regions.
+Jalview can calculate and display trees, providing interactive tree-based
+grouping of sequences though a tree viewer. All trees are calculated {\sl via}
+the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu.
+Trees can be calculated from distance matrices determined from \% identity or
+aggregate BLOSUM 62 score using either {\sl Average Distance} (UPGMA) or {\sl
+Neighbour Joining} algorithms. The input data for a tree is either the selected
+region or the whole alignment, excluding any hidden regions.
On calculating a tree, a new window opens (Figure \ref{trees1}) which contains
the tree. Various display settings can be found in the tree window {\sl View}
menu, including font, scaling and label display options, and the {\sl File
$\Rightarrow$ Save As} submenu contains options for image and Newick file
export. Newick format is a standard file format for trees which allows them to
-be exported to other programs. Jalview can also read in external trees in Newick format {\sl via} the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf names on imported trees will be matched to the associated alignment - unmatched
-leaves will still be displayed, and can be highlighted using the {\sl View
-$\Rightarrow$ Mark Unlinked Leaves} menu option.
+be exported to other programs. Jalview can also read in external trees in
+Newick format {\sl via} the {\sl File $\Rightarrow$ Load Associated Tree} menu
+option. Leaf names on imported trees will be matched to the associated alignment
+- unmatched leaves will still be displayed, and can be highlighted using the
+{\sl View $\Rightarrow$ Mark Unlinked Leaves} menu option.
\begin{figure}
sequences are automatically partitioned and coloured (Figure \ref{trees2}). To
group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
By Tree Order $\Rightarrow$ \ldots} alignment window menu option and choose the
-correct tree. The sequences will then be sorted according to the leaf order currently shown in the tree view. The coloured background to the sequence IDs can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the alignment window menu. Note that tree partitioning will also remove any groups and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to preserve these.
+correct tree. The sequences will then be sorted according to the leaf order
+currently shown in the tree view. The coloured background to the sequence IDs
+can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the
+alignment window menu. Note that tree partitioning will also remove any groups
+and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to
+preserve these.
\begin{figure}
\begin{center}
\exercise{Trees}{
-\exstep{ Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
+\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}).}
+\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the diferences between the two trees, calculated using different methods.}
\exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
\end{figure}
\exercise{Remove redundant sequences}{
+
+{\sl Note: Jalview 2.8 users - bugs in this version mean that the 'Unlinked leaves' markings will not be shown when sequences are removed during this exercise.}
+
\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.}
\subsection{Subdividing the alignment according to specific mutations}
It is often necessary to explore variations in an alignment that may correlate
-with mutations observed in a particular region; for example, sites
-exhibiting single nucleotide polymorphism, or residues involved in substrate
-recognition in an enzyme. One way to do this would be to calculate a tree using
-the specific region, and subdivide it in order to partition the alignment.
-However, calculating a tree can be slow for large alignments, and the tree may be difficult to partition when complex mutation patterns are being analysed. The {\sl Select $\Rightarrow$ Make groups for
-selection } function was introduced to make this kind of analysis easier. When
-selected, it will use the characters in the currently selected region to
-subdivide the alignment. For example, if a single column is selected, then the
-alignment (or each group defined on the alignment) will be divided into groups
-based on the residue or nucleotide found at that position. These new groups are
-annotated with the characters in the selected region, and Jalview's group based
-conservation analysis annotation and colourschemes can then be used to reveal
-any associated pattern of sequence variation across the whole alignment.
+with mutations observed in a particular region; for example, sites exhibiting
+single nucleotide polymorphism, or residues involved in substrate recognition in
+an enzyme. One way to do this would be to calculate a tree using the specific
+region, and subdivide it in order to partition the alignment.
+However, calculating a tree can be slow for large alignments, and the tree may
+be difficult to partition when complex mutation patterns are being analysed. The
+{\sl Select $\Rightarrow$ Make groups for selection } function was introduced to
+make this kind of analysis easier. When selected, it will use the characters in
+the currently selected region to subdivide the alignment. For example, if a
+single column is selected, then the alignment (or each group defined on the
+alignment) will be divided into groups based on the residue or nucleotide found
+at that position. These new groups are annotated with the characters in the
+selected region, and Jalview's group based conservation analysis annotation and
+colourschemes can then be used to reveal any associated pattern of sequence
+variation across the whole alignment.
\subsection{Automated annotation of Alignments and Groups}
-On loading a sequence alignment, Jalview will
-normally\footnote{Automatic annotation can be turned off in the
-{\sl Visual } tab in the {\sl Tools $\Rightarrow$ Preferences } dialog box.}
-calculate a set of automatic annotation rows which are shown below the
-alignment. For nucleotide sequence alignments, only an alignment
-consensus row will be shown, but for amino acid sequences,
-alignment quality (based on BLOSUM62) and physicochemical conservation will
+On loading a sequence alignment, Jalview will normally\footnote{Automatic
+annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
+$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
+rows which are shown below the alignment. For nucleotide sequence alignments,
+only an alignment consensus row will be shown, but for amino acid sequences,
+alignment quality (based on BLOSUM 62) 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."
-} 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
+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
right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
-Consensus} from the context menu. Quality is a measure of the inverse
-likelihood of unfavourable mutations in the alignment. Further details on these
+Consensus} from the context menu. Quality is a measure of the inverse likelihood
+of unfavourable mutations in the alignment. Further details on these
calculations can be found in the on-line documentation.
These annotations can be hidden and deleted but are only created on loading an
alignment. If they are deleted then the alignment should be saved and reloaded
-to restore them. Jalview provides a toggle to autocalculate a consensus
-sequence upon editing. This is normally selected by default, but can be turned off for large alignments
-{\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
+to restore them. Jalview provides a toggle to autocalculate a consensus sequence
+upon editing. This is normally selected by default, but can be turned off for
+large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
Consensus} menu option if the interface is too slow.
\subsubsection{Group Associated Annotation}
\exercise{Group conservation analysis}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc})} \exstep{Create a new view, and ensure the annotation panel is displayed, and
+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
}
\exstep{Clear the groups, and try to subdivide the alignment using two
non-adjacent columns.
-{\sl Hint: You may need to hide the intervening columns
-before you can select both of the columns that you wish to use to subdivide
-the alignment.}}
-\exstep{Switch back to the original view, and experiment with subdividing the tree groups made in the previous exercise.}
+
+{\sl Hint: You may need to hide the intervening columns before you can select
+both of the columns that you wish to use to subdivide the alignment.}}
+\exstep{Switch back to the original view, and experiment with subdividing
+the tree groups made in the previous exercise.}
}
\subsection{Other Calculations}
\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 {\sl Preferences} dialog box.
+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 {\sl Preferences} dialog box.
\exercise{Changing the Layout of the Web Services Menu}{
\label{changewsmenulayoutex}
\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment window�s {\sl Web Service} menu.}
+current layout of the alignment windowÔøΩs {\sl Web Service} menu.}
\exstep{Open the preferences dialog box and select the web services tab.}
\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
the {\sl Enable Enfin Services} checkboxes.}
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.}
+\label{jvjabawsconfig}
\end{center}
\end{figure}
+
+\subsubsection{Testing JABA services}
+The JABAWS configuration dialog shown in Figure \ref{jvjabawsconfig} has colour
+codes to indicate whether the Desktop can access the server, and whether all
+services advertised by the server are functional. The colour codes are:
+
+\begin{list}{$\bullet$}{}
+ \item Red - Server cannot be contacted or reports a connection error.
+ \item Amber - Jalview can connect, but one or more services are non-functional.
+ \item Green - Server is functioning normally.
+\end{list}
+ %TODO green and a tick, red and a cros, amber and a value indicating whether its all going
+
+Test results from JABAWS are reported on Jalview's console output (opened from
+the Tools menu). Tests are re-run every time Jalview starts, and when the
+[Refresh] button is pressed on the Jalview JABAWS configuration panel.
+
+\subsubsection{Resetting the JABA services setting to their defaults}
+Once you have configured a JABAWS server and selected the OK button of the
+preferences menu, the settings will be stored in your Jalview preferences file,
+along with any preferences regarding the layout of the web services menu. If
+you should ever need to reset the JABAWS server list to its defaults, use the
+`Reset Services' button on the Web Services preferences panel.
+
\subsection{Running your own JABA server}
You can download and run JABA on your own machine using the `VMWare' or
VirtualBox virtual machine environments. If you would like to learn how to do
}
}
-
-\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.
+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:
+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.
+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:
+(2005) {\sl Genome Research} {\bf 15} 330-340.} 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.}.
+Heringa {\sl JMB} {\bf 302} 205-217} and Clustal Omega.\footnote{Fast, scalable
+generation of high-quality protein multiple sequence alignments using Clustal
+Omega. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
+McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) {\sl Molecular
+Systems Biology} {\bf 7} 539
+\href{http://dx.doi.org/10.1038/msb.2011.75}{doi:10.1038/msb.2011.75}} 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, however Clustal Omega, which was released in 2011, is arguably the
+fastest and most accurate tool for protein multiple alignment.
To run an alignment web service, select the appropriate method from the {\sl
\subsubsection{Realignment}
-The re-alignment option is currently only supported by ClustalW. When performing a re-alignment, Jalview submits the current selection to the alignment service complete with any existing gaps. This approach is useful when one wishes to align additional sequences to an existing alignment without any further optimisation to the existing alignment. The Re-alignment service provided by ClustalW in this case is effectively a simple form of profile alignment.
+The re-alignment option is currently only supported by ClustalW and Clustal
+Omega. When performing a re-alignment, Jalview submits the current selection to
+the alignment service complete with any existing gaps. This approach is useful
+when one wishes to align additional sequences to an existing alignment without
+any further optimisation to the existing alignment. The Re-alignment service
+provided by ClustalW in this case is effectively a simple form of profile
+alignment.
\subsubsection{Alignments of sequences that include hidden regions}
-If the view or selected region that is submitted for alignment contains hidden regions, then {\bf only the visible sequences will be submitted to the service}. Furthermore, each contiguous segment of sequences will be aligned independently (resulting in a number of alignment `subjobs' appearing in the status window). Finally, the results of each subjob will be concatenated with the hidden regions in the input data prior to their display in a new window. This approach ensures that 1) hidden column boundaries in the input data are preserved in the resulting alignment - in a similar fashion to the constraint that hidden columns place on alignment editing (see Section \ref{lockededits}), and 2) hidden columns can be used to preserve existing parts of an alignment whilst the visible parts are locally refined.
+If the view or selected region that is submitted for alignment contains hidden
+regions, then {\bf only the visible sequences will be submitted to the service}.
+Furthermore, each contiguous segment of sequences will be aligned independently
+(resulting in a number of alignment `subjobs' appearing in the status window).
+Finally, the results of each subjob will be concatenated with the hidden regions
+in the input data prior to their display in a new window. This approach ensures
+that 1) hidden column boundaries in the input data are preserved in the
+resulting alignment - in a similar fashion to the constraint that hidden columns
+place on alignment editing (see Section \ref{lockededits}), and 2) hidden
+columns can be used to preserve existing parts of an alignment whilst the
+visible parts are locally refined.
\exercise{Multiple Sequence Alignment}{
\exstep{ Close all windows and open the alignment at {\sf
The presets are displayed in the JABA web services submenu, and can also be
accessed from the parameter editing dialog box, which is opened by selecting
-the `{\sl Edit settings and run ...}' option from the web service�s menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web serviceÔøΩs 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.
% }
% }
-
+\section{Protein alignment conservation analysis}
+\label{aacons}
+The {\sl Web Service $\Rightarrow$ Conservation} menu controls the computation
+of up to 17 different amino acid conservation measures for the current alignment
+view. The JABAWS AACon Alignment Conservation Calculation Service, which is used
+to calculate these scores, provides a variety of standard measures described by
+Valdar in 2002\footnote{Scoring residue conservation. Valdar (2002) {\sl
+Proteins: Structure, Function, and Genetics} {\bf 43} 227-241.} as well as an efficient implementation of the SMERFs
+score developed by Manning et al. in 2008.\footnote{SMERFS Score Manning et al. {\sl BMC
+Bioinformatics} 2008, {\bf 9} 51 \href{http://dx.doi.org/10.1186/1471-2105-9-51}{doi:10.1186/1471-2105-9-51}}
+
+\subsubsection{Enabling and disabling AACon calculations}
+When the AACon Calculation entry in the {\sl Web Services $\Rightarrow$
+Conservation} menu is ticked, AACon calculations will be performed every time
+the alignment is modified. Selecting the menu item will enable or disable
+automatic recalculation.
+
+\subsubsection{Configuring which AACon calculations are performed}
+The {\sl Web Services $\Rightarrow$ Conservation $\Rightarrow$ Change AACon
+Settings ...} menu entry will open a web services parameter dialog for the
+currently configured AACon server. Standard presets are provided for quick and
+more expensive conservation calculations, and parameters are also provided to
+change the way that SMERFS calculations are performed.
+AACon settings for an alignment are saved in Jalview projects along with the
+latest calculation results.
+
+\subsubsection{Changing the server used for AACon calculations}
+If you are working with alignments too large to analyse with the public JABAWS
+server, then you will most likely have already configured additional JABAWS
+servers. By default, Jalview will chose the first AACon service available from
+the list of JABAWS servers available. If available, you can switch to use
+another AACon service by selecting it from the {\sl Web Services $\Rightarrow$
+Conservation $\Rightarrow$ Switch Server} submenu.
+
+% TODO
\section{Protein Secondary Structure Prediction}
\label{protsspredservices}
Protein secondary structure prediction is performed using the
\end{list}
Jpred is launched in the same way as the other web services. Select {\sl Web
Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
-Secondary Structure Prediction}{\footnote JNet is the Neural Network based
+Secondary Structure Prediction}\footnote{JNet is the Neural Network based
secondary structure prediction method that the JPred server uses.} from the
alignment window menu (Figure \ref{jpred}).
A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
-\exstep{ Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear. Note that the number of sequences in the results window is many more than in the original alignment as JNet performs a PSI-BLAST search to expand the prediction dataset.
+\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear. Note that the number of sequences in the results window is many more than in the original alignment as JNet performs a PSI-BLAST search to expand the prediction dataset.
}
% TODO: check how long this takes - about 2 mins once it gets on the cluster.
\exstep{
}
}
+\section{Protein Disorder Prediction}
+\label{protdisorderpred}
+
+Disordered regions in proteins were classically thought to correspond to
+'linkers' between distinct protein domains, but disorder can also play a role in
+function. The {\sl Web Services $\Rightarrow$ Disorder} menu in the alignment window
+allows access to protein disorder prediction services provided by the configured
+JABAWS servers.
+
+\subsection{Disorder prediction results}
+Each service operates on sequences in the alignment to identify regions likely
+to be unstructured or flexible, or alternately, fold to form globular domains.
+As a consequence, disorder predictor results include both sequence features and
+sequence associated alignment annotation rows. Section \ref{featannot} describes
+the manipulation and display of these data in detail, and {\bf Figure
+\ref{alignmentdisorder}} demonstrates how sequence feature shading and
+thresholding (described in Section \ref{featureschemes}) can be used to
+highlight differences in disorder prediction across aligned sequences.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5in]{images/disorderpred.pdf}
+\caption{{\bf Shading alignment by sequence disorder}. Alignment of Interleukin IV homologs coloured with Blosum62 with protein disorder prediction sequence features overlaid, shaded according to their score. Borderline disordered regions appear white, reliable predictions are either Green or Brown depending on the type of disorder prediction. }
+\label{alignmentdisorder}
+\end{center}
+\end{figure}
+
+\subsubsection{Navigating large sets of disorder predictions}
+
+{\bf Figure \ref{alignmentdisorderannot}} shows a single sequence annotated with
+a range of disorder predictions. Disorder prediction annotation rows are
+associated with a sequence in the same way as secondary structure prediction
+results. When browsing an alignment containing large numbers of disorder
+prediction annotation rows, clicking on the annotation row label will highlight
+the associated sequence in the alignment display, and double clicking will
+select that sequence.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5in]{images/disorderpredannot.pdf}
+\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disorderd regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
+\label{alignmentdisorderannot}
+\end{center}
+\end{figure}
+
+
+\subsection{Disorder predictors provided by JABAWS 2.0}
+For full details of each predictor and the results that Jalview can display,
+please consult
+\href{http://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's
+protein disorder service documentation}. Short descriptions of the methods provided in JABAWS 2.0 are given below:
+
+\subsubsection{DisEMBL}
+\href{http://dis.embl.de/}{DisEMBL (Linding et al., 2003)} is a set of machine-learning based predictors trained to
+recognise disorder-related annotation found on PDB structures.
+
+\textbf{COILS} Predicts
+loops/coils according to DSSP
+definitions\footnote{DSSP Classifications of secondary structure are: $\alpha$-helix (H), 310-helix (G), $\beta$-strand (E)
+are ordered, and all other states ($\beta$-bridge (B), $\beta$-turn (T), bend (S),
+$\pi$-helix (I), and coil (C)) considered loops or coils.}. Features mark range(s) of
+residues predicted as loops/coils, and annotation row gives raw value
+for each residue. Value over 0.516 indicates loop/coil.
+
+\textbf{HOTLOOPS} constitute a refined subset of \textbf{COILS}, namely those loops with
+a high degree of mobility as determined from C$\alpha$ temperature factors (B
+factors). It follows that highly dynamic loops should be considered
+protein disorder. Features mark range(s) of residues predicted to
+be hot loops and annotation row gives raw value for each
+residue. Values over 0.6 indicates hot loop.
+
+\textbf{REMARK465} ``Missing
+coordinates in X-ray structure as defined by remark465 entries in PDB.
+Nonassigned electron densities most often reflect intrinsic disorder,
+and have been used early on in disorder prediction.'' Features give
+range(s) of residues predicted as disordered, and annotation rows gives
+raw value for each residue. Values over 0.1204 indicates disorder.
+
+\subsubsection{RONN {\sl a.k.a.} Regional Order Neural Network}
+\href{http://www.strubi.ox.ac.uk/RONN}{RONN} employs an approach
+known as the `bio-basis' method to predict regions of disorder in
+sequences based on their local similarity with a gold-standard set of
+disordered protein sequences. It yields a set of disorder prediction
+scores, which are shown as sequence annotation below the alignment.
+
+\textbf{JRonn}\footnote{JRonn denotes the score for this server because JABAWS
+runs a Java port of RONN developed by Peter Troshin and distributed as
+part of \href{http://www.biojava.org/}{Biojava 3}} Annotation Row gives RONN score for each residue in
+the sequence. Scores above 0.5 identify regions of the protein likely
+to be disordered.
+
+\subsubsection{IUPred}
+\href{http://iupred.enzim.hu/Help.php}{IUPred} employs
+an empirical model to estimate likely regions of disorder. There are
+three different prediction types offered, each using different
+parameters optimized for slightly different applications. It provides
+raw scores based on two models for predicting regions of `long
+disorder' and `short disorder'. A third predictor identifies regions
+likely to form structured domains.
+
+\textbf{Long disorder} Annotation rows predict
+context-independent global disorder that encompasses at least 30
+consecutive residues of predicted disorder. A 100 residue
+window is used for calculation. Values above 0.5 indicates the residue is
+intrinsically disordered.
+
+\textbf{Short disorder} Annotation rows predict for short, (and
+probably) context-dependent, disordered regions, such as missing
+residues in the X-ray structure of an otherwise globular protein.
+Employs a 25 residue window for calculation, and includes adjustment
+parameter for chain termini which favors disorder prediction at the
+ends. Values above 0.5 indicate short-range disorder.
+
+\textbf{Structured domains} are marked with sequence Features. These highlight
+likely globular domains useful for structure genomics investigation. Post-analysis of disordered region profile to find continuous regions
+confidently predicted to be ordered. Neighbouring regions close to
+each other are merged, while regions shorter than the minimal domain
+size of at least 30 residues are ignored.
+
+\subsubsection{GLOBPLOT}
+\href{http://globplot.embl.de/}{GLOBPLOT} defines regions of
+globularity or natively unstructured regions based on a running sum of
+the propensity of residues to be structured or unstructured. The
+propensity is calculated based on the probability of each amino acid
+being observed within well defined regions of secondary structure or
+within regions of random coil. The initial signal is smoothed with a
+Savitzky-Golay filter, and its first order derivative
+computed. Residues for which the first order derivative is positive
+are designated as natively unstructured, whereas those with negative
+values are structured.
+
+{\bf Disordered region} sequence features are created marking mark range(s) of residues with positive first order derivatives, and
+\textbf{Globular Domain} features mark long stretches of order. \textbf{Dydx} annotation rows gives the first order derivative of smoothed score. Values above 0 indicates
+residue is disordered.
+
+\textbf{Smoothed Score and Raw Score} annotation rows give the smoothed and raw scores used to create the differential signal that
+indicates the presence of unstructured regions. These are hidden
+by default, but can be shown by right-clicking on the alignment
+annotation panel and selecting \textbf{Show hidden annotation}.
\section{Features and Annotation}
\label{featannot}
\section{Importing features from databases}
\label{featuresfromdb}
-Jalview supports feature retrieval from public databases either directly or {\sl via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}). It includes built in parsers for Uniprot and EMBL records retrieved from the EBI. Sequences retrieved from these sources using the sequence fetcher (see Section \ref{fetchseq}) will already posess features.
+Jalview supports feature retrieval from public databases either directly or {\sl
+via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}).
+It includes built in parsers for Uniprot and EMBL records retrieved from the
+EBI. Sequences retrieved from these sources using the sequence fetcher (see
+Section \ref{fetchseq}) will already possess features.
\subsection{Sequence Database Reference Retrieval}
\label{fetchdbrefs}
do not match the coordinate system from which the features were defined, then
the features will be displayed incorrectly.
+\subsubsection{Viewing and exporting a sequence's database annotation}
+
+You can export all the database cross references and annotation terms shown in
+the sequence ID tooltip for a sequence by right-clicking and selecting the {\sl
+[Sequence ID] $\Rightarrow$ Sequence details \ldots} option from the popup menu.
+A similar option is provided in the {\sl Selection} sub-menu allowing you to
+obtain annotation for the sequences currently selected.
+
+\parbox[l]{3.4in}{
+The {\sl Sequence Details
+\ldots} option will open a window containing the same text as would be shown in
+the tooltip window, including any web links associated with the sequence. The
+text is HTML, and options on the window allow the raw code to be copied and
+pasted into a web page.}
+\parbox[c]{3in}{
+\centerline{\includegraphics[width=2.2in]{images/seqdetailsreport.pdf}}}
+
\subsubsection{Automatically discovering a sequence's database references}
Jalview includes a function to automatically verify and update each sequence's
start and end numbering against any of the sequence databases that the {\sl
Database IDs} option is selected, and then mousing over each sequence's ID.}
\exstep{Use the {\sl Webservice $\Rightarrow$ Fetch DB References} menu option to retrieve database IDs for the sequences.}
\exstep{Examine the tooltips for each sequence in the alignment as the retrieval progresses - note the appearance of new database references.}
-\exstep{Once the process has finished, save the alignment as a Jalview Project.
+\exstep{Once the process has finished, save the alignment as a Jalview Project.}
+\exstep{Now close all the windows and open the project again, and verify that the database references and sequence features are still present on the alignment}
-Now close all the windows and open the project again, and verify that the database references and sequence features are still present on the alignment}
+\exstep{View the {\sl Sequence details \ldots} report for the FER1\_SPIOL sequence and for the whole alignment. Which sequences have web links associated with them ?}
}
\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculate $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
}
}
+% \section{Working with RNA}
+% \label{workingwithrna}
+%
+% \subsection{RNA specific alignment colourschemes}
+% \label{rnacolschemes}
+%
+% \subsection{Exploring RNA secondary structure with VARNA}
+% \label{varna}
+%
+% \subsection{RNA Secondary structure annotation}
+% \subsubsection{Interactive creation of RNA secondary structure annotation}
+% \label{rnasecstrediting}
+%
+% \subsubsection{Import and export of RNA secondary structure annotation}
+% \label{rnasecstrio}
+
% \chapter{Advanced Jalview}
%
git://source.jalview.org / jalview-manual.git / blobdiff