{\Huge
-Jalview 2.10.00}
+Jalview 2.10.1}
\vspace{0.5in}
{\huge
Manual and Introductory Tutorial }
-\vspace{2.4in}
+\vspace{2.2in}
{\large
-David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,
+David Martin, James Procter
+Andrew Waterhouse, Saif Shehata, Nancy Giang
-Suzanne Duce and Geoff Barton
-
+Mungo Carstairs, Charles Ofoegbu, Kira Mour\~{a}o
+
+Suzanne Duce and Geoff Barton
}
-\vspace{1.2in}
+\vspace{0.9in}
School of Life Sciences, University of Dundee
Dundee, Scotland DD1 5EH, UK
-
-
\vspace{2in}
-Manual Version 1.8
+Manual Version 1.9.1
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-7th October 2016
+
+17th November 2017
\end{center}
\section{Introduction}
\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
+It is designed to be platform independent (running on Mac, MS Windows, Linux
and any other platforms that support Java). Jalview is capable of editing and
analysing large alignments (thousands of sequences) with minimal degradation in
-performance, and able to show multiple integrated views of the alignment and
-other data. Jalview can read and write many common sequence formats including
+performance. It is 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.
alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
-The Jalview Desktop in this version
-provides access to protein and nucleic acid sequence, alignment and structure
+The Jalview Desktop 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. It also
+\url{http://www.jmol.org}} and Chimera 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. It also
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
building, principal components analysis, physico-chemical property conservation
and sequence consensus analyses are built into the program. Web services enable
Jalview to access online alignment and secondary structure prediction programs,
-as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
+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 and UCSF Chimera\footnote{UCSF Chimera needs to be installed separately. It is available free for academic use from \url{https://www.cgl.ucsf.edu/chimera/download.html}.} 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}
\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
+appropriate, typically at the end of each section. The first few sections concerns the
basic operation of Jalview and should be sufficient for those who want to
launch Jalview (Section \ref{startingjv}), open an alignment (Section
\ref{loadingseqs}), perform basic editing (Section
\ref{selectingandediting}), colouring (Section \ref{colours}), and produce
publication and presentation quality graphical output (Section \ref{layoutandoutput}).
-In addition, the manual covers the additional visualization and
-analysis techniques available in Jalview. This includes working
-with the embedded Jmol molecular structure viewer, building and viewing trees and PCA
-plots, and using trees for sequence conservation analysis. An overview of
+The remaining sections of the manual cover the visualization and
+analysis techniques available in Jalview. These include working
+with the embedded Jmol molecular structure viewer (or UCSF Chimera), building
+and viewing trees and Principal Components Analysis (PCA) plots, and using
+trees for sequence conservation analysis. An overview of
the Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
the alignment and secondary structure prediction services are described
-in detail in Sections \ref{msaservices} and \ref{protsspredservices}. Section \ref{featannot} details the creation and visualization of sequence
-and alignment annotation. Section \ref{workingwithnuc} discusses
-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.
+in detail in Sections \ref{msaservices} and \ref{protsspredservices}
+respectively.
+Section \ref{featannot} details the creation and visualization of sequence,
+features and alignment annotation. Section \ref{workingwithnuc} discusses
+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
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) simultaneously.
+Keystroke combinations are denoted with a `-' symbol ({\em
+e.g.} [CTRL]-C means press [CTRL] and the `C' key simultaneously).
Menu options are given as a path from the menu
that contains them - for example {\sl File $\Rightarrow$ Input Alignment
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
+the JalviewLite applet, which has the same core editing, analysis and visualization capabilities. 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 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 program to handle the webstart
-file. If that is the case, then you will need to locate the {\bf javaws} program
+file. If that is the case, 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
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).
+from Jalview version 2.10.1).
%[figure 3 ]
\begin{figure}[htbp]
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
+\exstep {Dialog boxes
will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
Internet, click {\sl Open}. (Note you may be asked to update Java, if you agree
then it will automatically update the Java software). As Jalview opens, four demo
\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
+dialog box opens, untick the box adjacent to the `Open file' entry in the
`Visual' preferences tab.
Click {\sl OK} to save the preferences.}
\exstep{Launch another Jalview workbench from the web site by clicking on the
\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 (a downward arrow on the right hand side of the dialog
-box) to view the files, select exampleFile\_2\_7.jar, then click {\sl OK}.}
-{\bf Note:} Should you want to load your own
-sequence during the launch process, then go
+box) to view the files, select exampleFile\_2\_7.jar
+(\url{http://www.jalview.org/examples/exampleFile_2_3.jar})
+then click {\sl OK}.}
+{\bf Note:} Should you want to 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.
may want to move this from the downloads folder to another folder.
Opening from the jnlp file will allow Jalview to be launched offline.
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.}
}
\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
+$\Rightarrow$ Documentation} from the main desktop 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.
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: {\bf normal mode}, where
editing and navigation is performed using the mouse, and {\bf cursor mode}
where editing and navigation are performed using the keyboard. The {\bf F2 key}
- is used to switch between these two modes. With a Mac as the F2 is
- often assigned to screen brightness, one may often need to type {\bf function
- [Fn] key with F2} function
- [Fn]-F2.
+ is used to switch between these two modes.
+
+ {\em Note:} On MacBooks and other laptops with compact keyboards, you may need
+ to press the {\bf function key [Fn]} when pressing any of the numbered function
+ keys. So to toggle between keyboard and normal mode, press [Fn]-[F2].
+
\begin{figure}[htb]
\begin{center}
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
+{\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}
}}
Rapid movement to specific positions is accomplished as listed below:
\begin{list}{$\circ$}{}
\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to
-move to sequence (row). {\sl n}
+move to sequence (row) {\sl n}.
\item {\bf Jump to Column {\sl n}:} Type a number {\sl n} then press [C] to move to column {\sl n} in the alignment.
\item {\bf Jump to Residue {\sl n}:} Type a number {\sl n} then press [P] to move to residue number {\sl n} in the current sequence.
\item {\bf Jump to column {\sl m} row {\sl n}:} Type the column number {\sl m}, a comma, the row number {\sl n} and press [RETURN].
%TODO insert a figure for the Find dialog box
\exercise{Navigation}{
+\label{navigationEx}
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).
Documentation window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words.
-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+{\sl\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}.}
}
\section{Loading Sequences and Alignments}
%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
+ In most operating systems you can 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.
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
+simply drag the link or url from the address panel of your browser onto an
alignment or the Jalview desktop background and Jalview will load data from the
URL directly.
% (Figure \ref{drag})
by Jalview. The way to read sequences from these documents is to select the
data from the document and copy it to the clipboard. There are two ways to
do this. One is to right-click on the desktop background, and select the
-`Paste to new alignment' option in the menu that appears. The other is to select
+`Paste to new window' option in the menu that appears. The other is to select
{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
-main menu, and paste the sequences into the textbox window that will appear
-(Figure \ref{loadtext}). In both cases, presuming that they are in the right
-format, Jalview will happily read them into a new alignment window.
+main menu, paste the sequences into the text window that will appear, and select
+{\sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
+in the right format, Jalview will happily read them into a new alignment window.
%[fig 8]
\begin{figure}[htbp]
\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.
-
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
Click {\sl 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.
+{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and save the file to your desktop.
+your web browser and save the file to your desktop using {\sl File
+$\Rightarrow$ Save Page as}.
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 {\sl OK} to load.}
-\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.
+$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
+Select the file and click {\sl OK} to load.}
-(ii) Test the differences
-between (a) dragging the sequence onto the Jalview desktop and (b)
-dragging the sequence onto an existing alignment window.
-
-(iii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
-web browser. Drag the URL directly from browser onto Jalview desktop. (If
-the URL is downloaded, then locate the file in your
-download directory and open it in a text editor.)}
+\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+(i) Drag the alignment.fa file that you have just saved from its folder and
+drop it onto the Jalview desktop window, the alignment should open.
+
+(ii) Open
+\url{http://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
+browser. Test the differences
+between (a) dragging the URL directly from browser onto the Jalview
+desktop.
+(If the URL is downloaded, alternatively locate the file in your download
+directory and drag it onto the desktop.) (b) dragging the URL from
+browser onto the existing alignment.fa alignment window in the Jalview desktop.
+
+(iii) Open \url{http://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web
+browser. Note that this is a cDNA file. Drag the URL from
+browser onto the estrogenReceptorProtein.fa protein alignment window in
+the Jalview desktop. A dialogue box opens asking `Would you like to open as split
+window, with cDNA and protein linked?' select `Split Window' option. A
+split window opens in the Jalview desktop.
+}
\exstep{{\bf The text editor:} (i) 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 {\sl Paste to New Window} to new
-alignment option.
+Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
-(ii) 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).
+(ii) Place the mouse on the Jalview desktop and right-click the mouse
+to open the context window. Select the {\sl Paste to New Window} menu option.
-(iii) In the Desktop menu, select {\sl File
+(iii) In the Jalview 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.}
+Paste the clipboard into the large window using [CTRL]-V. Click {\sl New Window}
+and the alignment will be loaded.}
\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
-$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
-called Select Database Retrieval Source showing all the database
+$\Rightarrow$ Fetch Sequence(s)...} from the Jalview desktop menu. The {\sl
+Select Database Retrieval Source} dialog will open listing all the database
sources. Select the {\bf PFAM seed} database and click {\sl OK}.
-(ii)This opens another window called New Sequence Fetcher, enter the
-accession number {\bf PF03460} and click {\sl OK}. An alignment of about 174 sequences should
-load.}
+(ii) The {\sl New
+Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
+and click {\sl OK}.
+An alignment of about 174 sequences should load.}
\exstep{These can be viewed using the Overview window accessible from {\sl View
-$\Rightarrow$ Overview Window.}
-Several database IDs can be loaded by using semicolons to separate them.}
-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
-}
+$\Rightarrow$ Overview Window.}}
+{\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}} }
\section{Saving Sequences and Alignments}
\label{savingalignments}
-\subsection{Saving Alignments} 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
+\subsection{Saving Alignments} Jalview allows alignments to be saved to file
+in a variety of formats so they can be restored at a later date, passed to
+colleagues or analysed in other programs. From the alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box
will appear (Figure \ref{savealign}). You can navigate to an appropriate
directory in which to save the alignment. Jalview will remember the last filename
and format used to save (or load) the alignment, enabling you to quickly save
-the file during or after editing by using the {\sl File $\Rightarrow$ Save} entry.
+the file during or after editing by using the {\sl File $\Rightarrow$ Save}
+entry. 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
+Jalview offers several different formats in which an alignment can be saved.
+Of these, only the jalview project format (.jar or .jvp) will preserve the colours, groupings and other additional information in the alignment. The other formats
produce text files containing just the sequences with no visualization information, although some
allow limited annotation and sequence features to be stored (e.g. AMSA).
-Unfortunately only Jalview can read Jalview files. The {\sl File
-$\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
-other documents or web servers.
+Unfortunately, as far as we are aware only Jalview can read Jalview
+project files.
%[fig 10]
\begin{figure}[htbp]
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.}
+Jalview when working with large alignments in Jalview projects. See Section
+\ref{memorylimits} 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,
\exercise{Saving Alignments}{
\label{save}
-\exstep{Launch Jalview or use close all windows.
-Load the ferredoxin
-alignment from {\bf PFAM (seed)} data base using the PFAM seed accession number
-{\bf PF03460} (see Exercise \ref{load}). } \exstep{
+\exstep{Launch Jalview afresh, or use {\sl Desktop $\Rightarrow$ Window
+$\Rightarrow$ Close all }.}
+\exstep{Load the ferredoxin
+alignment ({\bf PF03460}) from {\bf PFAM (seed)} (see Exercise
+\ref{load}).
+} \exstep{
Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
location into which to save the alignment and select your preferred format. All
suitable folder.}
\exstep{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. }
-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
-}
+$\Rightarrow$ Load Project} menu option. Observe how many of the windows
+reopen. Are they the same as were saved. } {\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}.} }
\chapter{Selecting and Editing 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.
-{\bf To clear (unselect) the selection press the [ESC] (escape) key.}
+{\bf To clear (unselect) the selection press the [ESC] key.}
\subsection{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.
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}).
+Discontinuous regions can be selected by holding down [CTRL] and clicking on
+positions to add to the column selection. Note that each [CTRL]-Click (PC) or
+[CMD]-Click (Mac) changes the current selected sequence region to that column,
+it adds to the column selection.
+Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
%[fig 13]
\begin{figure}[htbp]
To select multiple complete sequences, click and drag the mouse down the
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
+with [SHIFT]-Click for continuous and [CTRL]-Click (or
+[CMD]-Click for Mac) to select discontinuous
ranges of sequences (Figure \ref{selectrows}).
%[fig 14]
$\Rightarrow$ Group $\Rightarrow$ Edit name and description of
current group}\footnote{In earlier versions of Jalview, this entry was variously
`Group', `Edit Group Name', or `JGroupXXXXX' (Where XXXXX was some serial
-number).} then enter a name for the group in the dialogue box which appears.
+number).} then enter a name for the group in the dialog box which appears.
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.
\exercise{Making Selections and Groups}{
\label{exselect}
-\exstep{Close windows.
-Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).
-Choose a residue and place the mouse
+\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+}
+\exstep{Selecting an arbitrary region. Choose a residue and place the mouse
cursor on it (residue information will show in alignment window status
bar).
-Click and drag the mouse to create a selection. As you drag, a red box
-will `rubber band' out to
+Click and drag the mouse to the bottom-right 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 borders the selected region.
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
+Hold down [CTRL] and then click on several sequences' IDs - 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{ Select columns by clicking on the Alignment Ruler. Note
+that the selected column is marked with a red box.
+Hold down [SHIFT] and click a column beyond. Note the selection expands to
+include all the sequences between the two positions on which you clicked.}
\exstep{Enter Cursor mode using [F2], or [Fn]-F2 for Macs.
Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
menus and pick an output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
\ldots} submenu.
}
-\exstep{In the Alignment output window that opens, manually edit the
-alignment before clicking the {\sl New Window} button, this opens the
-edited alignment in a new alignment window.} {\bf A video about this exercise is
-available on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
+\exstep{In the Alignment output window that opens, try manually editing the
+alignment before clicking the {\sl New Window} button. This opens the
+edited alignment in a new alignment window.} {\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
% more? change colouring style. set border colour.
}
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 {\sl New Window} button) or saving to a file with the {\sl File
+$\Rightarrow$ Save As } pulldown menu option from the text box.
\section{Reordering an 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.
\end{figure}
\exercise{Reordering the Alignment}{
-\exstep{Close all windows in Jalview from desktop menu. Load the ferredoxin
-alignment using the PFAM domain PF03460 from PFAM seed database.
-Select one of the sequence in the sequence ID panel, use the up and down
+\label{reorderex}
+\exstep{Close windows.
+
+Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+}
+\exstep{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 select two sequences separated by
one or more un-selected sequences, repeat using the [CTRL] key. Note how
multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}
-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
\subsection{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.
+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.
+Note, any alignment edits that affect the sequence will also affect the whole
+sequence group.
\exercise{Hiding and Revealing Regions}{
-\exstep{Close all windows, open the PFAM accession PF03460 from the PFAM (seed)
-database.
-Select a contiguous set of sequences by clicking and dragging on the sequence ID panel.
+\label{hidingex}
+\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+}
+\exstep{Select a contiguous set of sequences by clicking and dragging on the sequence ID panel.
Right click on the selected sequence IDs to bring up the sequence ID context
menu, select {\sl Hide Sequences}.
}
All Sequences.}) }
\exstep{
Repeat the process but use a non-contiguous set of sequences. Note that when
-multiple regions are hidden you may prefer to select {\sl
-Reveal Sequences} rather than {\sl Reveal All} option.
+multiple regions are hidden you can select either {\sl
+Reveal Sequences} to reveal the hidden sequences that were clicked, or {\sl
+Reveal All}.
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
Sequence ID and in the context menu select {\sl Reveal All}.}
-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
\section{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).
+
+\subsection{Undoing Edits}
+Alignment edits can be undone {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
+alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
+with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
+{\sl Undo} function only works for edits to the alignment or sequence ordering.
+Colouring of the alignment, showing and hiding of sequences or modification of
+annotation that only affect the alignment's display cannot
+be undone.
+
\subsection{Locked Editing}
\label{lockededits}
The Jalview alignment editing model is different to that used in other alignment
Gaps can be removed by dragging the residue to the immediate right of the gap
leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences).
-\subsection{Sliding Sequences}
-Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the entire selected sequences to the left
-or right (respectively). Slides occur regardless of the region selection -
-which, for example, allows you to easily reposition misaligned subfamilies
-within a larger alignment.
-% % better idea to introduce hiding sequences, and use the invert selection, hide
-% others, to simplify manual alignment construction
+\newpage
\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
-{You are going to manually reconstruct part of the example Jalview
+{
+\label{editingalignex}
+You are going to manually reconstruct part of the example Jalview
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
-{\sl Note: If you are using OSX, and a key combination - such as [CTRL]-A - does
- not work, then try the [CMD] key instead of [CTRL].}
+{\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
+for key combinations such as [CTRL]-A. }
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
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
O80429\_MAIZE
-(Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
+
+{\sl Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
deselect FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they
-begin at column 5 of the alignment view.}
+begin at column 5 of the alignment view.}}
\exstep{ Select all the visible
sequences (those not hidden) in the block by pressing [CTRL]-A.
backwards and replay the edits you have made.}
}
+\subsection{Sliding Sequences}
+Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
+sequences are selected will ``slide'' the entire selected sequences to the left
+or right (respectively). Slides occur regardless of the region selection -
+which, for example, allows you to easily reposition misaligned subfamilies
+within a larger alignment.
+% % better idea to introduce hiding sequences, and use the invert selection, hide
+% others, to simplify manual alignment construction
+
\subsection{Editing in Cursor mode}
Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
+
\exercise{Keyboard Edits}
-{This continues on from the previous exercise, and recreates the final part of the example ferredoxin
+{
+\label{keyboardsex}
+This continues on from the previous exercise, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
-{\bf Note:} For Mac users, [CTRL]-[SPACE] command
-has the same effect as the [SHIFT]-[SPACE] command mentioned in this exercise.
-Window users should use [SHIFT]-[SPACE] rather than the [CTRL]-[SPACE] command,
-as this command will close the window.
+{\bf Window users:} Please {\em only use} [SHIFT]-[SPACE] in this
+exercise.
+
+{\bf Mac users:} [CTRL]-[SPACE] can also be used instead of [SHIFT]-[SPACE].
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are
now aligned.}}
-\section{Undoing Edits}
-Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
-alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
-with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
-{\sl Undo} function only works for edits to the alignment or sequence ordering.
-Colouring of the alignment, showing and hiding of sequences or modification of
-annotation cannot be undone.
-
\chapter{Colouring Sequences and Figure Generation}
\label{colouringfigures}
\section{Colouring Sequences}
} \parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
+\subsubsection{User Defined}
+This dialog allows the user to create any number of named colour schemes at
+will. Any residue may be assigned any colour. The colour scheme can then be
+named. If you save the colour scheme, this name will appear on the Colour menu
+(Figure \ref{usercol}).
+
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2.5in]{images/col_user1.pdf}
+\includegraphics[width=2in]{images/col_user2.pdf}
+\includegraphics[width=1.75in]{images/col_user3.pdf}
+\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
+\label{usercol}
+\end{center}
+\end{figure}
+
\exercise{Colouring Alignments}{
\label{color}
-Note: Ensuring that the {\sl Apply Colour To All Groups} flag is not
-selected in {\sl Colour} menu in the alignment window.
-This must be turned {\sl off} specifically as it is on by default.
+Note: Before you begin this exercise, ensure that the {\sl Apply Colour
+To All Groups} flag is not selected in {\sl Colour} menu in the alignment window.
+% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
+% by default.
\exstep{Open a sequence alignment, for example the PFAM domain PF03460 in PFAM
seed database. Select the alignment menu option {\sl Colour $\Rightarrow$
-ClustalX} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
+Clustal} and 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)
\exstep{Keeping the same selection as before, colour the complete alignment except
the group using {\sl Colour $\Rightarrow$ Taylor}.
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
-Slide the selector in the Conservation Colour Increment dialogue box from side
+Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
Note: Feature colours overlay residue colouring. The features colours can be
toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
-{\bf A video about this exercise is
-available on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
-\subsubsection{User Defined}
-This dialogue allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu (Figure \ref{usercol}).
-
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.5in]{images/col_user1.pdf}
-\includegraphics[width=2in]{images/col_user2.pdf}
-\includegraphics[width=1.75in]{images/col_user3.pdf}
-\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
-\label{usercol}
-\end{center}
-\end{figure}
-
\exercise{User Defined Colour Schemes}{
-\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.}
+\label{colouex}
+\exstep{Load a sequence alignment. Ensure that the {\sl Colour $\Rightarrow$
+None} is selected. Select the alignment menu option {\sl Colour $\Rightarrow$
+User Defined}.
+A dialog window will open.}
\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.}
-\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.}
+\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialog window can now be closed.}
\exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}} }
\section{Formatting and Graphics Output}
\subsection{Multiple Alignment 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.
+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}{
+\parbox[c]{4in}{Alignment views are created using the {\sl View $\Rightarrow$
+New View} option of the alignment window or by pressing [CTRL]-T.
+This will create a new view with the same groups, alignment layout and display options as the current one.
+Pressing G will gather together Views as named tabs on the alignment window, and pressing X will expand gathered Views so they can be viewed
+simultaneously in their own separate windows. To delete a group, press [CTRL]-W.}\parbox[c]{2.75in}{
\begin{center}\centerline{
\includegraphics[width=2.5in]{images/mulv_tabs.pdf}}
\end{center}
annotation row labels to bring up the context menu, then 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}.}
+\exstep{Annotations can be reordered by clicking on the sequence name 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}.}
\exstep{Move the mouse to the top left hand corner of the annotation labels -
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 this icon up or down.}
-}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\subsection{Graphical Output}
\label{figuregen}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
\exercise{Graphical Output}{
+ \label{graphicex}
\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}.
Customise it how you wish but leave it unwrapped.
Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu.
Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
Preview (Mac OS X). Zoom in and note that the image has near-infinite
resolution.}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.
}
-The next chapters introduce Jalview's analysis features. Chapter \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. Chapter
-\ref{featuresfromdb} discusses the retrieval of database references and
-establishment of sequence coordinate systems for the retrieval and display of
-features from databases.
-Chapter \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Chapter \ref{aacons} introduces JABAWS AACon
-service for protein multiple alignment conservation analysis.
- In Chapter \ref{alignanalysis}, you will find
-descriptions and exercises on building and displaying trees, PCA analysis,
-alignment redundancy removal, pairwise alignments and alignment conservation
-analysis.
-Chapter \ref{wkwithstructure} introduces the structure visualization
-capabilities of Jalview.
-Chapter \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS protein disorder prediction
-services are introduced in Chapter \ref{protdisorderpred}.
-Chapter \ref{workingwithnuc} describes functions and visualization techniques relevant
-to working with nucleotide sequences, coding region annotation and nucleotide
-sequence alignments.
-Chapter \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Chapter \ref{jabaservices} explains how to
-configure the Jalview Desktop for access to new JABAWS servers.
+% left out for Glasgow 2016
+% \newpage
+%
+% \section{Summary - the rest of the manual}
+%
+% The first few chapters have covered the basics of Jalview operation: from
+% starting the program, importing, exporting, selecting, editing and colouring
+% aligments, to the generation of figures for publication, presentation and web
+% pages.
+%
+% The remaining chapters in the manual cover:
+%
+% \begin{list}{$\circ$}{}
+% \item{Chapter \ref{featannot} covers the creation, manipulation and visualisation
+% of sequence and alignment annotation, and retrieval of sequence and feature data
+% from databases.}
+% \item {Chapter \ref{msaservices} explores the range of multiple alignment
+% programs offered via Jalview's web services, and introduces the use of
+% AACon for protein multiple alignment conservation analysis.}
+% \item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for
+% multiple sequence alignment analysis, including trees, PCA, and alignment
+% conservation analysis. }
+% \item {Chapter \ref{3Dstructure} demonstrates the structure visualization
+% capabilities of Jalview.}
+% \item {Chapter \ref{proteinprediction} introduces protein sequence based
+% secondary structure and disorder prediction tools, including JPred.}
+% \item {Chapter \ref{dnarna} covers the special functions and
+% visualization techniques for working with RNA alignments and protein coding
+% sequences.}
+% \item {Chapter \ref{jvwebservices} provides instructions on the
+% installation of your own Jalview web services.}
+% \end{list}
\chapter{Annotation and Features}
\label{featannot}
but are shown mapped on to specific residues within the alignment.
Features and annotation can be interactively created, or retrieved from external
-data sources. Webservices like JNet (see \ref{jpred} above) can be used to analyse a
-given sequence or alignment and generate annotation for it.
+data sources. Webservices like JPred (see \ref{jpred} above) can be used to
+analyse a given sequence or alignment and generate annotation for it.
\section{Conservation, Quality and Consensus Annotation}
\subsection{Creating User Defined Annotation}
To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}).
-A dialogue box appears. Enter the label to use for this row and a new row will appear.
+A dialog box appears. Enter the label to use for this row and a new row will appear.
To create a new annotation, first select all the positions to be annotated on the appropriate row.
Right-clicking on this selection brings up the context menu which allows the insertion of graphics for secondary structure ({\sl Helix} or {\sl Sheet}),
-text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialogue box will appear,
+text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialog box will appear,
requesting the text to place at that position. After the text is entered, the selection can be removed and the annotation becomes clearly
visible\footnote{When annotating a block of positions, the text can be partly obscured by the selection highlight. Pressing the [ESC] key clears
the selection and the label is then visible.}. Annotations can be coloured or deleted as desired.
\exercise{Annotating Alignments}{
+ \label{annotatingalignex}
\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
-Right-click on the {\sl Conservation} annotation row to
-bring up the context menu and select {\sl Add New Row}. A dialogue box will
+Right-click on the label name of the {\sl Conservation} annotation row to
+bring up the context menu and select {\sl Add New Row}. A dialog box will
appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
}
Right click at this selection and select {\sl Label} from the context menu.
Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again
and select {\sl Colour}.
-Choose a colour from the colour chooser dialogue
+Choose a colour from the colour chooser dialog
and click {\sl OK}. Press [ESC] to remove the selection.
+
+{\sl Note: depending on your Annotation sort settings, your newly
+created annotation row might 'jump' to the top or bottom of the annotation
+panel. Just scroll up or down to find it again - the column you marked will
+still be selected. }
+
}
\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
context menu. You will be prompted for a label. Enter ``B" and press {\sl OK}. A new line showing the
sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet
arrow.
}
-\exstep{Right click on the title text of annotation row that you just created.
+\exstep{Right click on the title text in the annotation row that you just
+created.
Select {\sl Export Annotation} in context menu and, in the Export Annotation
dialog box that will open, select the Jalview format and click the {\sl [To Textbox]} button.
-
-The format for this file is given in the Jalview help. Press [F1] to open it, and find
-the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents
-pane. }
-
-\exstep{Export the file to a text editor and edit the file to change the name of the annotation
-row. Save the file and drag it onto the alignment view.}
-\exstep{Add an additional helix somewhere along the row by editing the file and
-re-importing it.
+(The format for this file is given in the Jalview help. Press [F1] to open it,
+and find the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents
+pane.) }
+
+\exstep{Open a text editor and copy the annotation text into the editor.
+Edit the text by changing the name of the annotation row and save the file.}
+\exstep{Drag the file onto the alignment in Jalview and check the annotation
+panel.} \exstep{Return to the text editor, add an additional helix somewhere
+along the row, save the file and re-importing it into Jalview as previously.
{\sl Hint: Use the Export Annotation function to view what helix annotation looks like in
a Jalview annotation file.}}
\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
-function to export all the alignment's annotation to a file.}
+function to export all the alignment's annotation to a file. Save the file.}
\exstep{Open the exported annotation in a text editor, and use the Annotation File Format
documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
they appear as several lines on a single line graph.
{\sl Hint: You need to change the style of annotation row in the first field of the annotation
-row entry in the file, and create an annotation row grouping to overlay the three quantitative
-annotation rows.}
+row entry in the file. Create an annotation row grouping to overlay the
+three quantitative annotation rows.}
}
+\exstep{{\bf Homework once you have completed exercise
+\ref{secstrpredex}:}
\label{viewannotfileex}
-{\sl Homework for after you have completed exercise \ref{secstrpredex}:}
-Recover or recreate the secondary structure prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export
-Annotation} function to view the Jnet secondary structure prediction annotation row. Note the
+
+Recover or recreate the secondary structure predictions that you made from
+JPred. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row.
+
+Note: the
SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
-annotation. }
+annotation.
+}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\section{Importing Features from Databases}
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.
+[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.
If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record.
\subsubsection{Rate of Feature Retrieval}
-Feature retrieval can take some time if a large number of sources is selected and if the alignment
-contains a large number of sequences.
+Feature retrieval can take some time if a large number of sources are selected
+and if the alignment contains a large number of sequences.
As features are retrieved, they are immediately added to the current alignment view.
The retrieved features are shown on the sequence and can be customised as described previously.
% }
\subsection{Creating Sequence Features}
-Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialogue box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
+Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialog box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
\begin{figure}[htbp]
\begin{center}
present it is usually necessary to customise the display. Jalview allows the
display, colour, rendering order and transparency of features to be modified
{\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
-brings up a dialogue window (Figure \ref{custfeat}) which allows the
+brings up a dialog window (Figure \ref{custfeat}) which allows the
visibility of individual feature types to be selected, colours changed (by
clicking on the colour of each sequence feature type) and the rendering order
modified by dragging feature types to a new position in the list. Dragging the
features file.
\exercise{Creating Features}{
+\label{featuresex}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in
iron binding so we will create them as features. Navigate to column 97, sequence 1.
Select the entire column by clicking in the ruler bar. Then right-click on the selection
to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}.
-A dialogue box will appear.
+A dialog box will appear.
}
\exstep{
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
the mouse cursor over the new features.
Note that the position given in the tool tip is the residue number, not the column number.
To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at column 95.
-Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
+Roll the mouse over the features and you will see that the feature has moved
+with the sequence. Delete the gap you created using {\sl Edit
+$\Rightarrow$ Undo}.
}
\exstep{
-Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature
+Add a similar feature to column 102. When the feature dialog box appears, clicking the Sequence Feature
Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
\exstep{Select {\sl View $\Rightarrow$ Feature Settings\ldots} from the
alignment window menu. The Sequence Feature Settings window will appear. Move
box for ``Iron binding site" under {\sl Display} and note that display of this
feature type is now turned off. Click it again and note that the features are
now displayed. Close the sequence feature settings box by clicking {\sl OK} or
-{\sl Cancel}.} }
+{\sl Cancel}.}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\chapter{Multiple Sequence Alignment}
\label{msaservices}
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 slow but the accurate. ClustalW is historically
+T-COFFEE is slow but accurate. ClustalW is historically
the most widely used. Muscle is fast and probably best for
smaller alignments. MAFFT is probably the best for large alignments,
however Clustal Omega, released in 2011, is arguably the fastest and most
accurate tool for protein multiple alignment.
+\section{Performing a multiple sequence alignment}
To run an alignment web service, select the appropriate method from the {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ \ldots} submenu (Figure
\ref{webservices}). For each service you may either perform an alignment with
using the `Algorithm ordering' entry within the {\sl Calculate $\Rightarrow$
Sort } sub menu.
-\subsubsection{Realignment}
+\subsection{Realignment to add sequences to an existing alignment}
The re-alignment option is currently only supported by Clustal
Omega and 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.
+current selection to the alignment service complete with any existing gaps.
+Realignment with ClustalW is useful when one wishes to align
+additional sequences to an existing alignment without any further optimisation
+to the existing alignment. ClustalO's realignment works by generating a
+probabilistic model (a.k.a HMM) from the original alignment, and then realigns
+{\bf all} sequences to this profile. For a well aligned MSA, this process
+will simply reconstruct the original alignment (with additional sequences), but
+in the case of low quality MSAs, some differences may be introduced.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{Alignments of Sequences that include Hidden Regions}
-If the view or selected region that is submitted for alignment contains hidden
+\subsection{Alignments of Sequences that include Hidden Regions}
+If the view or selected region 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).
columns can be used to preserve existing parts of an alignment whilst the
visible parts are locally refined.
-
-\subsection{Customising the Parameters used for Alignment}
-JABA web services allow you to vary the parameters used when performing a
-bioinformatics analysis. For JABA alignment services, this means you are
-usually able to modify the following types of parameters:
-\begin{list}{$\bullet$}{}
-\item Amino acid or nucleotide substitution score matrix
-\item Gap opening and widening penalties
-\item Types of distance metric used to construct guide trees
-\item Number of rounds of re-alignment or alignment optimisation
-\end{list}
-
-\subsubsection{Getting Help on the Parameters for a Service}
-Each parameter available for a method usually has a short description, which
-Jalview will display as a tooltip, or as a text pane that can be opened under
-the parameter's controls. In the parameter shown in Figure
-\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
-service can also be accessed, by right clicking the button and selecting a URL
-from the pop-up menu that will open.
+\subsection{Alignment Service Limits}
+Multiple alignment is a computationally intensive calculation. Some JABA server
+services and service presets only allow a certain number of sequences to be
+aligned. The precise number will depend on the server that you are using to
+perform the alignment. Should you try to submit more sequences than a service
+can handle, then an error message will be shown informing you of the maximum
+number allowed by the server.
\exercise{Multiple Sequence Alignment}{
+\label{msaex}
\exstep{ Close all windows and open the alignment at {\sf
http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}.
select and hide a few more columns in the N-terminal region, and submit the alignment to the
service again and explore the effect of local alignment on the non-homologous parts of the
N-terminal region.}
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
+\section{Customising the Parameters used for Alignment}
+
+JABA web services allow you to vary the parameters used when performing a
+bioinformatics analysis. For JABA alignment services, this means you are
+usually able to modify the following types of parameters:
+\begin{list}{$\bullet$}{}
+\item{Amino acid or nucleotide substitution score matrix}
+\item{Gap opening and widening penalties}
+\item{Types of distance metric used to construct guide trees}
+\item{Number of rounds of re-alignment or alignment optimisation}
+\end{list}
+\begin{figure}[htbc]
+\center{
+\includegraphics[width=3in]{images/jvaliwsparamsbox.pdf}
+\caption{{\bf Jalview's JABA alignment service parameter editing dialog box}.}
+\label{jwsparamsdialog} }
+\end{figure}
+
+\subsection{Getting Help on the Parameters for a Service}
+
+Each parameter available for a method usually has a short description, which
+Jalview will display as a tooltip, or as a text pane that can be opened under
+the parameter's controls. In the parameter shown in Figure
+\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
+service can also be accessed, by right clicking the button and selecting a URL
+from the pop-up menu that will open.
+
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2.5in]{images/clustalwparamdetail.pdf}
a preset, then it will be mentioned at the beginning of the job status file shown
in the web service job progress window.
-\subsubsection{Alignment Service Limits}
-Multiple alignment is a computationally intensive calculation. Some JABA server
-services and service presets only allow a certain number of sequences to be
-aligned. The precise number will depend on the server that you are using to
-perform the alignment. Should you try to submit more sequences than a service
-can handle, then an error message will be shown informing you of the maximum
-number allowed by the server.
-
\subsection{User Defined Presets}
Jalview allows you to create your own presets for a particular service. To do
this, select the `{\sl Edit settings and run ...}' option for your service,
description for the parameter set, which will be shown in the tooltip for the
parameter set's entry in the web services menu.
-\begin{figure}[htbc]
-\center{
-\includegraphics[width=3in]{images/jvaliwsparamsbox.pdf}
-\caption{{\bf Jalview's JABA alignment service parameter editing dialog box}.}
-\label{jwsparamsdialog} }
-\end{figure}
-
\subsubsection{Saving Parameter Sets}
When creating a custom parameter set, you will be asked for a file name to save
it. The location of the file is recorded in the Jalview user preferences in the
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 $\Rightarrow$
+\subsection{Enabling and Disabling AACon Calculations}
+When the AACon Calculation entry in the {\sl Web Service $\Rightarrow$
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
+\subsection{Configuring which AACon Calculations are Performed}
+The {\sl Web Service $\Rightarrow$ 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
AACon settings for an alignment are saved in Jalview projects along with the
latest calculation results.
-\subsubsection{Changing the Server used for AACon Calculations}
+\subsection{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 $\Rightarrow$
+another AACon service by selecting it from the {\sl Web Service $\Rightarrow$
Conservation $\Rightarrow$ Switch Server} submenu.
\chapter{Analysis of Alignments}
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 chapter \ref{jvwebservices}.
-In this section, we describe the built-in analysis capabilities common to both
-the Jalview Desktop and the JalviewLite applet.
+Jalview {\sl via} web services - and found under the
+{\sl Web Service} menu. In this section, we describe the built-in analysis
+capabilities common to both the Jalview Desktop and the JalviewLite applet.
\section{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
+Principal components analysis calculations create 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 each sequence as a point in
3D `similarity space'. Sets of similar sequences tend to lie near each other in
this space.
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
+Jalview provides two different options for the PCA calculation: SeqSpace and
+Jalview mode. In SeqSpace mode, PCAs are computed using the identity matrix, and
+gaps are treated as 'the unknown residue' (this actually differs from the
+original SeqSpace paper, and will be adjusted in a future version of Jalview).
+In Jalview mode, PCAs are computed using the chosen score matrix - which for
+protein sequences, defaults to BLOSUM 62, and for nucleotides, is the
+DNA identity matrix that also treats Us and Ts as identical, to support analysis
+of both RNA and DNA alignments. The {\sl Change Parameters} allows the
+calculation method and score models to be changed.\footnote{See
\url{http://www.jalview.org/help/html/calculations/pca.html}.}
\subsubsection{The PCA Viewer}
the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
\exercise{Principal Component Analysis}
-{ \exstep{Load the alignment at
+{\label{pcaex}
+\exstep{Load the alignment at
\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
-\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principal Component
-Analysis}.
-A new window will open. Move this window within the desktop so that the tree,
-alignment and PCA viewer windows are all visible.
+\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window and a dialogue box will open. Select the Principal Component Analysis option
+and then click the Calculate button.}
+\exstep{Move
+this window within the desktop so that the alignment and PCA viewer windows are 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 the sequences on the
-alignment.
-} \exstep{ Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using BLOSUM62}. A new tree window will appear.
-Place the mouse cursor on the tree window so that the
-tree partition location will divide the alignment into a number of groups, each of a different colour.
+alignment.}
+\exstep{Use the [ESC] key to deselect sequence selection.
+Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment window. In dialogue box select Neighbour
+Joining and in the drop-down list select BLOSUM62. Click the Calculate button
+and a tree window will open.}
+\exstep{Place the mouse cursor on the tree so that the
+tree partition divides the tree into a number of groups, each with a
+different (arbitrarily selected) 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.}
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
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
+menu, including font, scaling and label display options. 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
- unmatched leaves will still be displayed, and can be highlighted using the
{\sl View $\Rightarrow$ Mark Unlinked Leaves} menu option.
+\exercise{Trees}
+{\label{treeex}
+{\sl Ensure that you have at least 1G memory available in Jalview.
+(Start with link:
+\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
+or in the table in the Development section of the Jalview web site
+(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds}), go
+to ``latest official build'' row and in the ``Webstart'' column, click
+on ``2G''.)}
+
+\exstep{Open the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+
+\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window and a dialogue box opens. In the tree section select Neighbour
+Joining, in the drop-down list select BLOSUM62 and click the Calculate
+button. A tree window will open.}
+
+\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.}
+
+
+\exstep{In the tree window, select {\sl View $\Rightarrow$ Sort Alignment
+by Tree}. The sequences are reordered to match the order in the tree and groups
+ are formed implicitly. Alternatively in the alignment window, select
+{\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$
+ Neighbour Joining Tree using BLOSUM62 from...}.}
+
+\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window. In the dialogue box, select Average Distance and in the drop down
+list select BLOSUM62. Click the Calculate button and a new
+tree window will appear. The group colouring makes it easy to see the differences between the two
+trees calculated by the different methods.}
+
+\exstep{In the alignment window, select sequence 2 from
+column 60 to sequence 12 and column 123. Select {\sl Calculate $\Rightarrow$
+Tree or PCA..}. , in the dialogue box select Neighbour Joining and
+BLOSUM62, then click the Calculate button.
+ A tree will appear containing 11 sequences. It has been coloured
+ according to the already selected groups from the first tree and is calculated purely from the residues
+ in the selection.}
+
+Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the
+alignment for the calculation of trees.
+
+{\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+
+}
\begin{figure}
\begin{center}
\includegraphics[width=2.5in]{images/trees1.pdf}
\includegraphics[width=2.5in]{images/trees2.pdf}
\includegraphics[width=1.25in]{images/trees4.pdf}
-\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees.
+\caption{{\bf Calculating Trees} Jalview provides a range of options
+for calculating trees.
Jalview can also load precalculated trees in Newick format (right).}
\label{trees1}
\end{center}
% move to ch. 3 ?
%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
-\subsubsection{Recovering input Data for a Tree or PCA Plot Calculation}
+\subsubsection{Recovering input data for a Tree or PCA Plot Calculation}
\parbox[c]{5in}{
The {\sl File $\Rightarrow$ Input Data } option will open a new alignment window containing the original data used to calculate the tree or PCA plot (if available). This function is useful when a tree has been created and then the alignment subsequently changed.
}
\parbox[c]{1.25in}{\centerline{\includegraphics[width=1.25in]{images/pca_fmenu.pdf}
}}
-\subsubsection{Changing the associated View for a Tree or PCA Viewer}
+\subsubsection{Changing the associated view for a Tree or PCA Viewer}
\parbox[c]{4in}{
The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display according to the colouring and selection state of the newly associated view.
} \parbox[c]{3in}{\centerline{
Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
can help when working with larger alignments.
-\exercise{Trees}
-{Ensure that you have at least 1G memory available in Jalview.
-{\sl (Start with link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
-or in the Development section of the Jalview web site
-(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
-in the table, go to ``latest official build'' row and ``Webstart'' column, click on ``G2''.)}
-\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 tree window opens.}
-\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.}
-\exstep{In the alignment window, 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.
-Alternatively in the tree window, select {\sl View $\Rightarrow$ Sort Alignment
-by Tree}.}
-\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 differences between the two
-trees calculated by the 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. The tree contains 11 sequences. It has been coloured according to the already
- selected groups from the first tree and is calculated purely from the residues
- in the selection.}
-
-Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the
-alignment for the calculation of trees.
-
-{\bf A video about this exercise is available on the Jalview website at
-\url{http://www.jalview.org/training/Training-Videos}.}
-}
-\exercise{Pad Gaps in an Alignment}{
-\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. In alignment window, ensure that the {\sl Edit $\Rightarrow$
-Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the
-alignment.}
-\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using BLOSUM62}.
+%\exercise{Pad Gaps in an Alignment}{
+%\exstep{Open the alignment at
+% \textsf{http://www.jalview.org/tutorial/alignment.fa}. In alignment window, ensure that the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the
+%alignment.}
+%\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
+%Neighbour Joining Using BLOSUM62}.
-A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
+%A warning dialog box {\bf ``Sequences not aligned'' } appears because the
+% sequences input to the tree calculation are of different lengths. }
-\exstep{Select {\sl Edit $\Rightarrow$ tick Pad Gaps } and perform the
-tree calculation again. This time a new tree should appear - because padding
-gaps ensures all the sequences are the same length after editing.}
-{\sl Pad Gaps } option
-can be set in Preferences using
-{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
+%\exstep{Select {\sl Edit $\Rightarrow$ tick Pad Gaps } and perform the
+%tree calculation again. This time a new tree should appear - because padding
+%gaps ensures all the sequences are the same length after editing.}
+%{\sl Pad Gaps } option
+%can be set in Preferences using
+%{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
-{\bf A video about this exercise is available on the Jalview website at
-\url{http://www.jalview.org/training/Training-Videos}.}
-}
+%{\bf See the video at:
+%\url{http://www.jalview.org/training/Training-Videos}.}
+%}
-\exercise{Tree Based Conservation Analysis}{
+ \exercise{Tree Based Conservation Analysis}{
\label{consanalyexerc}
\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher.
-Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}, set {\sl Conservation} shading threshold at around 20. }
-\exstep{Build a Neighbour joining tree using Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using BLOSUM62}.}
-\exstep{Use the mouse cursor to select a point on the tree to partition the
-alignment into several sections.}
+Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}, set
+ {\sl Conservation} shading threshold at around 20. }
+ \exstep{Build a Neighbour joining tree by selecting {\sl Calculate
+ $\Rightarrow$ Tree or PCA..}. in the alignment window. In the dialogue box, select Neighbour
+Joining and in the drop-down
+list select BLOSUM62, then click the Calculate button.}
+\exstep{Use the cursor to select a point on the tree to partition the
+alignment into groups.}
\exstep {Select {\sl View $\Rightarrow$ Sort Alignment By Tree} option in the
-tree window to re-order the sequences in the alignment using the calculated
-tree.
-Examine the variation in colouring between different groups of sequences in the alignment
-window. }
-\exstep {You may find it easier to browse the alignment if you first uncheck the
-{\sl Annotations $\Rightarrow$ Show Annotations} option. Open the
-Overview Window within the View menu to aid navigation.}
+tree window to re-order the sequences in the alignment.
+Examine the variation in colouring between different groups of sequences in the
+ alignment window. }
+\exstep {You may find it easier to browse the alignment if you first uncheck
+ the {\sl Annotations $\Rightarrow$ Show Annotations} option. Open the
+Overview Window from the View menu to aid navigation.}
\exstep{Try changing the colourscheme of the residues in the alignment to
BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected).}
{\sl Note: You may want to save the alignment and tree as a project file, since
it is used in the next set of exercises. }
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
\exercise{Remove Redundant Sequences}{
-
+\label{redundantex}
\exstep{Using the alignment generated in the previous exercise (exercise
\ref{consanalyexerc}).
In the alignment window, you may need to deselect groups using Esc key.}
}
\exercise{Group Conservation Analysis}{
+\label{conservationex}
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc}).}
\exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to
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.}
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
\end{figure}
-\chapter{Working with 3D structures}
-\label{3Dstructure}
-Jalview can interactively view 3D structure using Jmol or Chimera. Whether Jmol or Chimera is
-the default structure viewer of choice is set from {\sl Preferences}, go
-to {\sl Tools $\Rightarrow$ Preferences\ldots} and select either JMOL or
-CHIMERA in the {\sl Structure} tab.
-
% To review, Chapter \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. Chapter
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
-\section{Working with Structures}
+\chapter{Working with 3D structures}
+\label{3Dstructure}
\label{wkwithstructure}
-Jalview facilitates the use of protein structures for the analysis of alignments
-by providing a linked view of structures associated with sequences in
-the 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}).
-
-\subsection{Automatic Association of PDB Structures with Sequences}
-Jalview can automatically determine which structures are associated with a
-sequence in a number of ways.
-\subsubsection{Discovery of PDB IDs from Sequence Database Cross-references}
-If a sequence has an ID from a public database that contains cross-references to
-the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl Structure $\Rightarrow$
-Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (Figure \ref{auto}). Jalview will attempt to associate the
-sequence with a Uniprot sequence and from there discover any associated PDB
-structures. This takes a few seconds and applies to all sequences in the
-alignment which have valid Uniprot IDs. On moving the cursor over the sequence
-ID the tool tip\footnote{Tip: The sequence ID tooltip can often become large for
-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.
+Jalview facilitates the use of 3D structure data for the analysis of alignments
+by providing a linked view of structures associated with the aligned sequences.
+It also allows sequence, secondary structure and B-factor data to be imported
+from structure files, and supports the use of the EMBL-EBI's SIFTS database to
+construct accurate mappings between UniProt protein sequences and structures
+retrieved from the PDB.
+
+\section{Molecular graphics systems supported by Jalview}
+Jalview can interactively view 3D structure using Jmol, a Java based molecular
+viewing program\footnote{See the Jmol homepage \url{http://www.jmol.org} for
+more information.} integrated with Jalview.\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 using the sequence alignment.} It also supports the use of UCSF
+Chimera, a powerful molecular graphics system that needs separate installation.
+Jalview can also read PDB and mmCIF format files directly to extract sequences
+and secondary structure information, and retrieve records from the European
+Protein Databank (PDBe) using the Sequence Fetcher (see \ref{fetchseq}).
+
+\subsection{Configuring the default structure viewer}
+\label{configuring3dviewer}
+To configure which viewer is used when creating a new
+structure view, open the Structures preferences window {\sl via} {\sl Tools $\Rightarrow$ Preferences\ldots} and
+select either JMOL or CHIMERA as the default viewer. If you select Chimera,
+Jalview will search for the installed program, and if it cannot be found,
+you will be prompted to locate the Chimera binary, or alternately, open the UCSF
+Chimera download page to obtain the software.
+
+\section{Automatic Association of PDB Structures with Sequences}
+Jalview will attempt to automatically determine which structures are associated
+with a sequence via its ID, and any associated database references. To do this
+for a particular sequence or the current selection, open the Sequence ID popup
+menu and select {\sl View 3D Structure}, to open the 3D Structure Chooser.
+%(Figure\ref{auto}).
+
+When the structure chooser is first opened, if no database identifiers are
+available, Jalview will automatically perform a database reference
+retrieval (See \ref{fetchdbrefs}) to discover identifiers for the
+sequences to use to search the PDB. This can take a
+few seconds for each sequence and will be performed for all selected
+sequences.\footnote{After this is done, you can see the added database
+references in a tool tip by mousing over the sequence ID. You can use the {\sl
+View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show Db References }
+submenu option to enable or disable these data in the tooltip.}
+
+Once the retrieval has finished, the structure chooser dialog will show any
+available PDB entries for the selected sequences.
-\begin{figure}[htbp]
-\begin{center}
-%TODO fix formatting
-\parbox{1.5in}{
-{\centering
-\begin{center}
-\includegraphics[width=1.5in]{images/auto1.pdf}
-\end{center}}
-} \parbox{3.25in}{
-{\centering
-\begin{center}
-\includegraphics[scale=0.5]{images/auto2.pdf}
-\end{center}
-}
-} \parbox{1.5in}{
-{\centering
-\begin{center}
-\includegraphics[width=1.5in]{images/auto3.pdf}
-\end{center}
-}
-}
-
-\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence.
-After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and
-any associated PDB structures (right).}
-\label{auto}
-\end{center}
-\end{figure}
+%
+% \begin{figure}[htbp]
+% \begin{center}
+% %TODO fix formatting
+% \begin{center}
+% \includegraphics[width=3.5in]{images/pdbstructurechooser.pdf}
+% \end{center}
+%
+%
+% \caption{{\bf The PDB Structure Chooser dialog.} }
+% \label{auto}
+% \end{center}
+% \end{figure}
-\subsubsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
+\subsection{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 you have PDB files stored on your computer named the same way as the
+sequences in the alignment, then you can drag them 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, and offer a dialog like the one
+in Figure \ref{multipdbfileassocfig}.
If no associations are made, then sequences extracted
from the structure will be simply added to the alignment. However, if only
sequence within a local directory. Check out
\href{http://issues.jalview.org/browse/JAL-801}{Jalview issue 801}}
+After associating sequences with PDB files, you can view the PDB structures by
+opening the Sequence ID popup
+menu and selecting {\sl View 3D Structure}. The PDB files you loaded will be
+shown in the {\bf Cached Structures} view, after selecting it from the drop down
+menu in the dialog box.
+
% there is no mention of the other footnote (#3) that appears saying: Tip: The sequence ID tooltip can often become large for heavily cross-referenced sequence IDs. Use the ...
% JBP: yes there is - under 'Discovery of ' subsection.
\begin{figure}[htbp]
\end{figure}
-\subsection{Viewing Structures}
-\label{viewAllStructures}
-The structure viewer can be launched in two ways from the sequence ID context
-menu. To view a particular structure associated with a sequence in the
-alignment, simply select it from popup menu's associated structures submenu in
-{\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 {\bf currently selected}
-sequences have structures associated, the {\sl Structure } submenu of the
-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.
-
-In both cases, each structure to be displayed will be downloaded or loaded from
+\section{Viewing Structures}
+\label{structurechooser}
+The structure viewer is launched via the Sequence ID context
+menu. To view structures associated with a sequence or a selected set of
+sequences in the alignment, simply right click the mouse to open the context
+menu, and select {\sl 3D Structure data \ldots} to open the Structure Chooser
+dialog box.
+
+If any of
+the {\bf currently selected} sequences have structures in the PDB,
+they will appear in the Structure Chooser dialog box. The structures can be ranked by
+different parameters, but are by default ordered according to their PDB
+quality score.
+
+To view one or more structures, simply click {\sl
+View} to open a structure viewer containing the structures selected in the
+dialog. If several structures were picked, these will be shown
+superposed according to the alignment.
+You may find Jalview has already picked the best structure - using one of the
+criteria shown in the dropdown menu (e.g. 'Best Quality', which is picked by
+default). However, you are free to select your own.
+
+The structure(s) to be displayed will be downloaded or loaded from
the local file system, and shown as a ribbon diagram coloured according to the
associated sequence in the current alignment view (Figure \ref{structure}
(right)). The structure can be rotated by clicking and dragging in the structure
window. The structure can be zoomed using the mouse scroll wheel 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,
\begin{figure}[htbp]
\begin{center}
-\parbox{3in}{
+\parbox{4in}{
{\centering
\begin{center}
-\includegraphics[scale=0.5]{images/structure1.pdf}
+\includegraphics[width=4in]{images/structure1.pdf}
\end{center}
}
}
-\parbox{3.2in}{
+\parbox{2.2in}{
{\centering
\begin{center}
-\includegraphics[width=3in]{images/structure2.pdf}
+\includegraphics[width=2.2in]{images/structure2.pdf}
\end{center}
}
}
-\caption{{\bf Structure visualization} The structure viewer is launched from the sequence ID context menu (left) and allows the structure to be visualized using the embedded Jmol molecular viewer (right). }
+\caption{{\bf Structure visualization} Structure viewers are launched from
+the 3D Structure chooser dialog (left). Jalview shows the displayed structures
+coloured according the alignment view (right). }
\label{structure}
\end{center}
\end{figure}
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
+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 }
automatic application of colour schemes when new structure data is added, or
when associated alignment views are modified.
-\exercise{Viewing Structures in Jmol viewer}{\label{viewingstructex}
+\exercise{Viewing Structures with the integrated Jmol Viewer}{
+\label{viewingstructex}
\exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar}.}
\exstep{Right-click on the
sequence ID label of {\sl FER1\_SPIOL} to open
-the context menu. Select {\sl 3D Structure}, this
-opens a Structure Chooser window, select { \sl 1A70} and click {\sl View}.
-
-{\sl Note: the Structure Chooser interface
-provides a smart technique for selecting PDB structures by queryingthe meta-data
-of structures. Extra information can be including in this window by checking boxes
-in the columns of the ``Customise Displayed Options'' tab}.
+the ID popup menu and select {\sl 3D Structure}. After a short pause, a
+Structure Chooser dialog will open for the sequence, listing available
+structure data from the PDB. Select { \sl 1A70} from the list and click {\sl
+View}.
+
+{\sl The Structure Chooser dialog presents available PDB structures
+by querying the EMBL-EBI's PDBe web API. Extra information can be
+including in this window by checking boxes in the columns of the ``Customise Displayed Options'' tab}.
% JBP Note: Bug JAL-1238 needs to be fixed ASAP
}
\exstep{By default the Jmol
\exstep{In the alignment window, use the {\sl File $\Rightarrow$ Save As.. }
function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
Verify that the Jmol display is as it was when you just saved the file.}
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
-\exercise{Setting Chimera as the default 3D Structure Viewer}{\label{viewingchimera}
+\exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{
+\label{superpositionex}
+
+\exstep{Continue with the Jalview project created in exercise
+\ref{viewingstructex}}
+
+\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL
+by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$
+3D Structure Data \ldots } }
+
+\exstep{Pick 1A70 from the Structure Chooser dialog, and click the {\bf View}
+button. Jalview will give you the option of aligning the
+structure to the one already open. To superimpose the structure associated with
+FER1\_MAIZE with the one associated with FER1\_SPIOL, press {\sl Yes}.
+
+{\sl The Jmol view should update to show both structures, and one will be
+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 (you can do this via {\sl View $\Rightarrow$ Hide $\Rightarrow$
+All but selected region}).}
+\exstep{Select the newly created view in the {\sl Jmol $\Rightarrow$ Superpose
+With } submenu, and then recompute the superposition with {\sl Jmol
+$\Rightarrow$ Align Structures}.
+
+{\sl Note how the molecules shift position when superposed with only a small
+region of the alignment.}}
+
+\exstep{Compare RMSDs obtained when superimposing molecules with
+columns 121-132 and with the whole alignment.}
+
+\exstep{The RMSD report can be
+viewed by right clicking the mouse on Jmol window, and select {\sl
+Console} from the menu (if nothing is shown, recompute the superposition after
+displaying the console).
+
+Which view do you think give the best 3D superposition, and why ?} }
+
+\exercise{Setting Chimera as the default 3D Structure Viewer}{
+\label{viewingchimera}
Jalview supports molecular structure
visualization using both Jmol and Chimera 3D viewers. Jmol is the default
viewer, however Chimera can be set up as the default choice from Preferences.
the Chimera structure viewer sits outside the Jalview desktop and a Chimera
view window sits inside the Jalview desktop.}
-{\bf A video about this exercise is available on the Jalview website at
-\url{http://www.jalview.org/training/Training-Videos}.} }
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}}
+
\subsection{Superimposing Structures}
\label{superposestructs}
Jalview can employ Jmol's 3D fitting routines\footnote{See
\href{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}
for more information.} to recreate 3D structure superpositions based on the
-correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view happens automatically if a
-structure is added to an existing Jmol display using the {\sl Structure
-$\Rightarrow$ View PDB Structure $\Rightarrow$ ..}. A new Jmol view containing
-superposed structures can also be created using the {\sl Structure
-$\Rightarrow$ View all {\bf N} PDB Structures} option (when {\bf {\sl N}}
-$>$ 1) if the current selection contains two or more sequences with associated
+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 3D Structure } option in the Sequence ID popup menu to open the
+Structure Chooser dialog box.
+Select the structures required and select {\sl View}. A new Jmol view
+opens containing superposed structures if the current selection contains two or more sequences with associated
structures.
\subsubsection{Obtaining the RMSD for a Superposition}
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 outputted to the Jalview
+Full information about the superposition is also reported on 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.
directly compared.
In order to recompute a superposition after changing a view or editing the
-alignment, select the {\sl Jmol $\Rightarrow$ Align sequences } menu option. The {\sl
-Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
+alignment, select the {\sl Jmol $\Rightarrow$ Align Structures} menu option.
+The {\sl Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
associated alignments and views are to be used to create the set of
correspondences. This menu is useful when composing complex superpositions
involving multi-domain and multi-chain complexes, when correspondences may be
Note that these menu options appear when you have two or more structures in one Jmol viewer.
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
-\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
-left was used by Jalview to superpose structures associated with the
-FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
-used for superposition are rendered as a cartoon, the remainder rendered in
-wireframe. The RMSD between corresponding positions in the structures before and
-after the superposition is shown in the Jmol console.}
-\label{mstrucsuperposition}
-\end{center}
-\end{figure}
-
\subsection{Colouring Structure Data Associated with Multiple Alignments and
Views} Normally, the original view from which a particular structure view was
opened will be the one used to colour structure data. If alignments involving
Note that the {\sl Select many views} option is useful if you have different
views that colour different areas or domains of the alignment. This option is
-further explored in Section \ref{complexstructurecolours}.
+further explored in exercise \ref{complexstructurecolours}.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
+\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
+left was used by Jalview to superpose structures associated with the
+FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
+used for superposition are rendered as a cartoon, the remainder rendered in
+wireframe. The RMSD between corresponding positions in the structures before and
+after the superposition is shown in the Jmol console.}
+\label{mstrucsuperposition}
+\end{center}
+\end{figure}
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\exercise{Aligning Structures using the Ferredoxin
-Sequence Alignment}{\label{superpositionex}
-
-\exstep{Continue with the Jalview project created in exercise
-\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
-IDs associated with the FER1\_MAIZE sequence.}
-\exstep{Once discovery has completed, use the {\sl
-View PDB Structure} submenu to view one of the PDB file associated with
-FER1\_MAIZE (eg. 3B2F). Jalview will give you the option of aligning the
-structure to the one already open. To superimpose the structure associated with FER1\_MAIZE with the one
-associated with FER1\_SPIOL, press the {\sl Yes} button.
-
-{\sl The Jmol view will update to show both structures, and one will be
-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
-recompute the superposition using just columns 121-132 of the alignment
-(The easiest way to achieve this is to select column 121-132, and in the View
-menu selected ``All but selected region'' from the Hide options).
-
-{\sl Note how the molecules shift position when superposed using a short part of
-the two structures.}}
-\exstep{Compare the initial and final RMSDs for superimposing molecules with
-the small section and with the whole alignment.}
-\exstep{The RMSD report can be
-viewed by right clicking the mouse on Jmol window, and select ``Show" and
-``Measurements". Which view do you think give the best 3D
-superposition, and why ?} }
-
\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
The ability to control which multiple alignment view is used to colour
\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
+\exstep{Launch the Jalview desktop and ensure you have at least 1G of
free memory available.
+{\sl See section \ref{memorylimits} for how to do this or click the following
+link:
+
+\url{http://www.jalview.org/services/launchApp?jvm-max-heap=2G} }}
+
+\exstep{Retrieve the following PFAM alignments from the {\bf PFAM (full)} source
+:
+
+PF02008 PF01426 PF00145 (enter all three - they
+will each be retrieved into their own alignment window).}
+
+\exstep{Drag the URL or file of the structure you
+downloaded in step 1 onto one of the alignments to associate it with the mouse sequence in that Pfam domain family.}
+
+\exstep{Locate every DNMT1\_MOUSE sequence in the
+alignment by opening the Find dialog box via {\sl Select
+$\Rightarrow$ Find}. Search using the text DNMT1\_MOUSE. For
+each one, open the Structure Chooser dialog box by right clicking the mouse on
+sequence name to open the context menu and select {\sl
+$\Rightarrow$ 3D Structure Data}.
+Select `Cached Structures' from
+the drop-down menu in the Structure Chooser dialog box, select the
+DNMT1\_MOUSE.pdb structure, and click {\bf View}.
+
+{\em Part of the newly opened structure will be coloured the same way as
+the associated DNMT1\_MOUSE sequence is in the alignment view.}
+
+{\bf WARNING: do not select all sequences and open the Structure Chooser
+!} {\em This will cause Jalview to attempt to discover all structures for
+sequences in the alignment.}
+}
+\exstep{Repeat the previous two steps for each of the other
+alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and
+hitting the `View' button on the Structure Chooser dialog. Jalview will ask if
+you wish to create a new Jmol view, respond {\bf `Yes'} each time. This will
+ensure each sequence fragment is associated with the {\bf same} Jmol view. }
+
+\exstep{Pick a different
+colourscheme for each alignment, and use the {\sl Colour by ..} submenu to
+ensure they are all used to colour the complex shown in the Jmol window.
+
+{\sl The different shading schemes will allow regions of strong physicochemical conservation are
+highlighted on the domains in the structure.}
+}
-{\sl Use the following webstart link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}
-{\sl Alternatively in the Development section of the Jalview web site
-(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
-in the ``latest official build'' row in the table, go to the
-``Webstart'' column, click on ``G2''.}}
-\exstep{Retrieve the following {\bf full} PFAM alignments: PF02008, PF01426
-(make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.} \exstep{Drag the URL or file of the structure you downloaded in
-step 1 onto one of the alignments to associate it with the mouse sequence in
-that Pfam domain family.}
-\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
-ID popup menu's {\sl Structure} submenu to view the DNMT1\_MOUSE structure for the associated mouse sequence. When given the option, {\bf view all of the structures in the same Jmol viewer}. Check the contents of the {\sl View $\Rightarrow$ Colour by ..} submenu to see what alignments can be used to
-colour the sequence.}
-\exstep{Repeat the previous two steps for each of
-the other alignments. In each case, when performing the `View DNMT1\_MOUSE.pdb'
-step, Jalview will ask if you wish to create a new Jmol view. You should
-respond `No', {\bf ensuring that each sequence fragment is associated with the same Jmol view}.}
-\exstep{Pick a different colourscheme for each alignment, and use the {\sl
-Colour by ..} submenu to ensure they are all used to colour the complex shown
-in the Jmol window.}
\exstep{The final step needed to reproduce the shading in Figure
\ref{mviewalcomplex} is to use the {\sl Colour $\Rightarrow$ By
-Annotation } option in each alignment window to shade the alignment by the
-{\bf Conservation} annotation row. This function was described in section
-\ref{colourbyannotation}.
+Annotation\ldots } option in each alignment window to shade the alignment by the
+{\bf Conservation} annotation row (introduced in section
+\ref{colourbyannotation}).
-Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu option, or you may not see any colour changes in the associated structure.
+Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu
+option, or you may not see any colour changes in the associated structure.
-{\sl Note: Choose a different shading scheme for each
-alignment so that the regions of strong physicochemical conservation are highlighted. This
-kind of shading will reveal conserved regions of interaction between domains
-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 Examine the regions strongly coloured at the interfaces between each
+protein domain, and the DNA binding region. What do you think these patterns
+mean? } }
+\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
}
% TODO
-\chapter{Protein Prediction Analysis}
+\chapter{Protein sequence analysis and structure prediction}
\label{proteinprediction}
+
+Many of Jalview's sequence feature and annotation capabilities were developed to
+allow the results of sequence based protein structure prediction methods to be
+visualised and explored. This chapter introduces services integrated with the
+Jalview Desktop for predicting protein secondary structure and protein disorder.
+
\section{Protein Secondary Structure Prediction}
\label{protsspredservices}
Protein secondary structure prediction is performed using the
-Jpred\footnote{{\sl ``The Jpred 3 Secondary Structure Prediction Server''} Cole, C., Barber, J. D. and Barton, G. J. (2008) {\sl Nucleic Acids Research} {\bf 36}, (Web Server Issue) W197-W201
+Jpred\footnote{{\sl ``The Jpred 3 Secondary Structure Prediction Server''} Cole,
+C., Barber, J. D. and Barton, G. J. (2008) {\sl Nucleic Acids Research} {\bf
+36}, (Web Server Issue) W197-W201
{\sl ``Jpred: A Consensus Secondary Structure Prediction Server''} Cuff, J. A.,
Clamp, M. E., Siddiqui, A. S., Finlay, M. and Barton, G. J. (1998) {\sl
the same criteria as above, then the alignment will be used for a JPred
prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
\end{list}
-Jpred is launched in the same way as the other web services. Select {\sl Web
-Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
-Secondary Structure Prediction}\footnote{JNet is the Neural Network based
-secondary structure prediction method that the JPred server uses.} from the
-alignment window menu (Figure \ref{jpred}).
-A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
-predictions are included as annotations. Consult the Jpred documentation for
-information on interpreting these results.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.25in]{images/jpred1.pdf}
-\includegraphics[width=3in]{images/jpred2.pdf}
-\caption{{\bf Secondary Structure Prediction} Status (left) and results (right) windows for JNet predictions. }
-\label{jpred}
-\end{center}
-\end{figure}
-
-\subsubsection{Hidden Columns and JNet Predictions}
-\label{hcoljnet}
-Hidden columns can be used to exclude parts of a sequence or profile from the
-input sent to the JNet service. For instance, if a sequence is known to include
-a large loop insertion, hiding that section prior to submitting the JNet
-prediction can produce different results. In some cases, these secondary structure predictions can be more reliable for sequence on either side of the insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results returned from the service will
-be mapped back onto the visible parts of the sequence, to ensure a single frame
-of reference is maintained in your analysis.
-
-\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 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.
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
+
+{\sl Note: The annotation panel can get quite busy during this exercise. Try
+hiding some annotations rows by right clicking
+the mouse in the annotation label panel and select the ``Hide this row'' option.
+The Annotations dropdown menu on the alignment window also provides options for
+reordering and hiding autocalculated and sequence associated annotation. }
+
\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.
+clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$
+Secondary Structure Prediction $\Rightarrow$ JPred 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. The results
-from the prediction are visible in the annotation panel. Jnet secondary
+JPred performs a PSI-BLAST search to expand the prediction dataset. The results
+from the prediction are visible in the annotation panel. JPred secondary
structure prediction annotations are examples of sequence-associated alignment annotation. }
% TODO: check how long this takes - about 2 mins once it gets on the cluster.
\exstep{
-Select a different sequence and perform a JNet prediction in the same way. There will probably be minor differences in the predictions.
+Select a different sequence and perform a JPred prediction in the same way.
+There will probably be minor differences in the predictions.
}
\exstep{
Select the sequence used in the second sequence prediction by clicking on its
by right clicking the mouse to open the context menu, and select the {\sl Add
Reference Annotation} option.
-{\bf All} the JNet predictions for the sequences will now be visible in the
+{\bf All} the JPred predictions for the sequences will now be visible in the
original alignment window.}
-{\sl Note: The annotation panel can get quite busy and it may be
-helpful to hide some of the annotations rows, by right clicking the mouse in
-the annotation label panel and select ``Hide this row'' option in the context
-menu}. }
+{\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
+follow the instructions to view the Jalview annotations file created from the annotations
+generated by the JPred server for your sequence.
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\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}
+\includegraphics[width=2.25in]{images/jpred1.pdf}
+\includegraphics[width=3in]{images/jpred2.pdf}
+\caption{{\bf Secondary Structure Prediction} Status (left) and results (right)
+windows for JPred predictions. }
+\label{jpred}
\end{center}
\end{figure}
-\subsubsection{Navigating Large Sets of Disorder Predictions}
-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.
+Jpred is launched in the same way as the other web services. Select {\sl Web
+Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JPred
+Secondary Structure Prediction}\footnote{JNet is the Neural Network based
+secondary structure prediction method that the JPred server uses.} from the
+alignment window menu (Figure \ref{jpred}).
+A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
+predictions are included as annotations. Consult the Jpred documentation for
+information on interpreting these results.
+
+\subsection{Hidden Columns and JPred Predictions}
+\label{hcoljnet}
+Hidden columns can be used to exclude parts of a sequence or profile from the
+input sent to the JNet service. For instance, if a sequence is known to include
+a large loop insertion, hiding that section prior to submitting the JNet
+prediction can produce different results. In some cases, these secondary
+structure predictions can be more reliable for sequence on either side of the
+insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results
+returned from the service will be mapped back onto the visible parts of the
+sequence, to ensure a single frame of reference is maintained in your analysis.
+
+\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 Service $\Rightarrow$ Disorder} menu in the alignment window
+allows access to protein disorder prediction services provided by the configured
+JABAWS servers.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
+\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 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.
+
+
+\subsection{Navigating Large Sets of Disorder Predictions}
+
+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.
\subsection{Disorder Predictors provided by JABAWS 2.0}
For full details of each predictor and the results that Jalview can display,
range(s) of residues predicted as disordered, and annotation rows gives
raw value for each residue. Values over 0.1204 indicates disorder.
+\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{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
annotation panel and selecting \textbf{Show hidden annotation}.
\exercise{Protein Disorder Prediction}{
-%\label{protdispredex}
-
-\exstep{Open the alignment at:
-\url{http://www.jalview.org/tutorial/interleukin7.fa}. } also available at
+\label{protdisorderex}
+{\sl Before starting this exercise, make sure you enable the \protect{`Add
+Temperature Factor'} option in your {\bf Structures} preferences. }
+\exstep{Open the alignment using
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
-\url{http://www.jalview.org/tutorial/training-materials/2014/Dundee/Oct/interleukin7.fa}
+\exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
+$\Rightarrow$ Disorder Prediction }.}
-\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services
-$\Rightarrow$ Disorder Prediction } submenu.}
-
-\exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
-IDs} to retrieve all the PDB structures for the sequences.}
-
-\exstep{Open and align
-the structures for all sequences. ({\sl Hint: see \ref{viewAllStructures} to see
-how to do this.})}
+\exstep{Select all the sequences. Open the Structure Chooser by placing
+the mouse in the Sequence ID panel, right clicking the mouse and select
+{\sl$\Rightarrow$ 3D Structure Data\ldots }. Select all structures in the list.
+Hit the View button to retrieve and show all PDB structures for the sequences.}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
-\exstep{Apply the IUPred disorder prediction method.}
-\exstep{Use the {\sl Per
-sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
-the sequences by the long and short disorder predictors.
-
-Do the two methods agree with the structure ?}}
+\exstep{Features on sequences can conceal other colouring. This can be
+toggled off by selecting {\sl View
+$\Rightarrow$ Show Sequence Features}.}
+\exstep{Apply the IUPred disorder prediction method. Tick the
+the {\sl Per sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog
+box. Then shade the sequences by the long and short disorder predictors. {\sl
+Note how well the disordered regions predicted by each method agree
+with the structure.}}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\chapter{DNA and RNA Sequences}
\label{dnarna}
and alignments. Jalview recognises nucleotide sequences and alignments based on
the presence of nucleotide symbols [ACGT] in greater than 85\% of the
sequences. Built in codon-translation tables can be used to translate ORFs
-into peptides for further analysis. EMBL nucleotide records retrieved {\sl via} the
+into peptides for further analysis. ENA nucleotide records retrieved {\sl via} the
sequence fetcher (see Section \ref{fetchseq}) are also parsed in order to
identify codon regions and extract peptide products. Furthermore, Jalview
records mappings between protein sequences that are derived from regions of a
\subsection{Linked DNA and Protein Views}
\parbox{3.5in}{
-Views of alignments involving DNA sequences are linked to views of alignments containing their peptide products in a similar way to views of protein sequences and views of their associated structures. Peptides translated from cDNA that have been fetched from EMBL records for DNA contigs are linked to their `parent' coding regions. Mousing over a region of the peptide highlights codons in views showing the original coding region.
+Views of alignments involving DNA sequences are linked to views of alignments containing their peptide products in a similar way to views of protein sequences and views of their associated structures. Peptides translated from cDNA that have been fetched from ENA records for DNA contigs are linked to their `parent' coding regions. Mousing over a region of the peptide highlights codons in views showing the original coding region.
}\parbox{3in}{
\begin{center}
%\begin{figure}[htbp]
}
-\subsection{Coding Regions from EMBL Records}
+\subsection{Coding Regions from ENA Records}
-Many EMBL records that can be retrieved with the sequence fetcher contain exons.
-Coding regions will be marked as features on the EMBL nucleotide sequence, and
+Many ENA records that can be retrieved with the sequence fetcher contain exons.
+Coding regions will be marked as features on the ENA nucleotide sequence, and
Uniprot database cross references will be listed in the tooltip displayed when
the mouse hovers over the sequence ID. Uniprot database cross references
-extracted from EMBL records are sequence cross references, and associate a
+extracted from ENA records are sequence cross references, and associate a
Uniprot sequence's coordinate system with the coding regions annotated on the
-EMBL sequence. Jalview utilises cross-reference information in two ways.
+ENA sequence. Jalview utilises cross-reference information in two ways.
\subsubsection{Retrieval of Protein or DNA Cross References}
-The {\sl Calculate $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the protein product(s).
+The {\sl Calculate $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for ENA sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the ENA record for each residue in the protein product(s).
\subsubsection{Retrieval of Protein Features on Coding Regions}
-The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments.
+The Uniprot cross-references derived from ENA records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments.
This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig.
Jalview will use the Uniprot accession numbers associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using
the coding region location.
\includegraphics[width=5in]{images/dnadasfeatures.pdf}
\caption{Uniprot and PDB sum features retrieved and mapped onto
-coding regions of EMBL record V00488 (an earlier version of Jalview is shown
+coding regions of ENA record V00488 (an earlier version of Jalview is shown
here).}
\end{center}
\exercise{Visualizing Protein Features on Coding Regions}
{
-\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
+\label{protfeatureex}
+\exstep{Use the sequence fetcher to retrieve ENA record D49489.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the
alignment view format to {\sl Wrapped} mode so the distinct exons can be seen.}
\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots}
\subsection{Performing RNA Secondary Structure Predictions}
Secondary structure consensus calculations can be performed by enabling the
-VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+VIENNA service {\sl via} the {\sl Web Service $\Rightarrow$ Secondary
Structure} menu. These consensus structures are created by analysing the
covariation patterns in all visible sequences on the alignment. For more
information see the VIENNA documentation.
\includegraphics[width=5in]{images/rnaViennaServiceWindow.pdf}
\caption{Secondary structure consensus calculations can be performed by enabling the
-VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+VIENNA service {\sl via} the {\sl Web Service $\Rightarrow$ Secondary
Structure} menu.}
\end{center}
\exercise{Viewing RNA Structures}
{ \label{viewingrnaex}
-\exstep{Import RF00162 from Rfam (Full) using {\sl Fetch sequence(s)} option in
-{\sl File} menu.}
-\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
-the secondary structure annotation provided by Rfam.}
+\exstep{Import RF00162 from the Rfam (Seed) source using {\sl Fetch sequence(s)}
+from the Desktop's File menu.}
+
+\exstep{Select {\sl Colour by RNA Helices} to
+shade the alignment by the secondary structure annotation provided by Rfam.}
\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
$\Rightarrow$ RNA Secondary Structure}.
In the VARNA Structures Manager toggle between (i) secondary structure
(alignment) (with gaps) and (ii) trimmed secondary structure (alignment).
Explore the difference between trimmed and untrimmed views.
-Click on different residues and located them in the sequence alignment window.}
+Click on different residues in the VARNA diagram - you should also see them
+highlighted and selected in the sequence alignment window.}
\exstep{In the VARNA Structures Manager, right click on display window to
-bring up the pop up context menu. Investigate option within File, Export, Display
-and Edit sections.}
+bring up the pop up context menu. Explore the options within the File, Export,
+Display and Edit sections.
+
+{\em VARNA views are stored in Jalview project files, in the same way as 3D
+structure views produced by Jmol and Chimera.}}
-\exstep{Perform a secondary structure prediction in {\sl Web Services}. Enable
-the VIENNA consensus calculation via the {\sl Web Services} menu and select
-Change RNAAIiFold settings option.}
+\exstep{Enable the calculation and display of an RNAAliFold secondary structure
+prediction for the alignment by selecting {\sl Web Service $\Rightarrow$ Secondary
+Structure Prediction $\Rightarrow$ RNAAliFold }.}
% Compare this with the annotationline provided by Rfam.
-\exstep{Edit the VIENNA calculation settings to show
+\exstep{Edit the RNAAliFold calculation settings to show
Base Pair probabilities. Explore how editing the alignment affects the consensus
calculation.}
-\exstep{Import 2GIS from PDB database using {\sl Fetch sequence(s)} option.}
+\exstep{Import 2GIS from the PDB database into a new window with {\sl Fetch
+sequence(s)}.}
+
\exstep{Click on a sequence in Sequence ID panel and select {\sl Structure
$\Rightarrow$ View Structure $\Rightarrow$ 2GIS}, to view the structure in Jmol
window. Click on different residues and located them in the sequence alignment window.}
+
%\exstep{Add and link a Jmol structure view
%for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
%structure along-side the consensus structure for the alignment by adding
\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
+VirtualBox virtual machine environments. If you would like to do
this, there are full instructions at the
\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
WARNING: This is large (about 300MB) and will take some time to download.
}
\exstep{Unpack the archive's contents to a place on your machine with at least
-2GB of free space.
-
-(On Windows, right click on the archive, and use the 'Extract archive..' option).
+2GB of free space (On Windows, right click on the archive, and use the 'Extract
+archive..' option).
}
\exstep{Open the newly extracted directory and double click the VMWare virtual
machine configuration file (jabaws.vcf). This will launch the VMWare player.
git://source.jalview.org / jalview-manual.git / blobdiff