{\Huge
-Jalview 2.9.0b2}
+Jalview 2.10.0}
\vspace{0.5in}
{\huge
\vspace{1.2in}
-College of Life Sciences, University of Dundee
+School of Life Sciences, University of Dundee
Dundee, Scotland DD1 5EH, UK
\vspace{2in}
-Manual Version 1.6
+Manual Version 1.8
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-18th February 2016
+7th October 2016
\end{center}
alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
-Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
+The Jalview Desktop in this version
provides access to protein and nucleic acid sequence, alignment and structure
databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
-\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. A
-Distributed Annotation System (DAS) client\footnote{jDAS - released under Apache license (v2.0) at \url{http://code.google.com/p/jdas}} which facilitates the retrieval and display of third party sequence
-annotation in association with sequences and any associated structure. It also
-provides a graphical user interface for the multiple sequence alignment, conservation analysis and protein disorder prediction methods provided as {\bf Ja}va {\bf B}ioinformatics
-{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS). JABAWS\footnote{released under GPL at \url{http://www.compbio.dundee.ac.uk/jabaws}} is a system for running bioinformatics programs that you can download and run on your own machine or cluster, or install on compute clouds.
+\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
+provides a graphical user interface for the multiple sequence alignment, conservation analysis
+and protein disorder prediction methods provided as {\bf Ja}va {\bf B}ioinformatics
+{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS). JABAWS\footnote{released under GPL at \url{http://www.compbio.dundee.ac.uk/jabaws}} is a system for
+running bioinformatics programs that you can download and run on your own machine or cluster, or install on compute clouds.
\subsection{Jalview's Capabilities}
% TODO add references to appropriate sections for each capability described here.
Jim Procter to re-engineer the original program to introduce contemporary developments
in bioinformatics and take advantage of the latest web and Java technology.
Jalview's development has been supported from 2009
-by awards from the BBSRC's Tools and Resources fund, and, since 2014, a Wellcome Trust Biomedical Resource grant\footnote{Wellcome grant number 101651/Z/13/Z}. In 2010, 2011, and 2012, Jalview benefitted from the
+onwards by BBSRC funding, and since 2014 by a
+Wellcome Trust Biomedical Resource grant\footnote{Wellcome grant number 101651/Z/13/Z}. In 2010, 2011, and 2012, Jalview benefitted from the
\href{http://code.google.com/soc/}{Google Summer of Code}, when Lauren Lui and Jan Engelhardt introduced new features for handling RNA alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
This tutorial is written in a manual format with short exercises where
appropriate, typically at the end of each section. This chapter concerns the
basic operation of Jalview and should be sufficient for those who want to
-load Jalview (Section \ref{startingjv}), open an alignment (Section \ref{loadingseqs}), perform basic editing and colouring (Section \ref{selectingandediting} and Section \ref{colours}), and produce publication
-and presentation quality graphical output (Section \ref{layoutandoutput}).
-
-Chapter \ref{analysisannotation} covers the additional visualization and
-analysis techniques that Jalview provides. This includes working with the
-embedded Jmol molecular structure viewer, building and viewing trees and PCA
+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 Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
the alignment and secondary structure prediction services are described
-in detail in Sections \ref{msaservices} and \ref{protsspredservices}. Following
-this, Section \ref{featannot} details the creation and visualization of sequence
-and alignment annotation, and the retrieval of sequences and annotation from
-databases and DAS Servers. Finally, Section \ref{workingwithnuc} discusses
+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.
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).
+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
When the application is launched with webstart, two dialogs may appear before
the application starts. If your browser is not set up to handle webstart, then
clicking the launch link may download a file that needs to be opened
-manually, or prompt you to select the correct program to handle the webstart
+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
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
\exercise{Launching Jalview from the Jalview Website}{
\label{start}
-\exstep{Open the Jalview web
-site \href{http://www.jalview.org}{(www.jalview.org)}
+\exstep{Open the Jalview web site
+\href{http://www.jalview.org}{(www.jalview.org)}
in your web browser. Launch Jalview by clicking on the
pink `Launch Jalview' Desktop button in the top right hand corner. This
will download and open a jalview.jnlp webstart file.}
-\exstep {Dialogue boxes
+\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 Open. (Note you maybe asked to update Java, if you agree then it
-will automatically update the Java software). As Jalview opens, four demo
+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
Jalview windows automatically load.}
\exstep {If
you are having trouble, it may help changing the browser you are using, as the browsers and
-it's version may affect this process.}
+its version may affect this process.}
\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. A `Preference'
-dialogue box opens, untick the box adjacent to the `Open file' entry in the
+dialog box opens, untick the box adjacent to the `Open file' entry in the
`Visual' preferences tab.
-Click OK to save the preferences.}
+Click {\sl OK} to save the preferences.}
\exstep{Launch another Jalview workbench from the web site by clicking on the
pink Launch button.
The example alignment should not be loaded as Jalview starts up.}
\exstep{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
-the URL history button on the right hand side of the dialog box to view the
-files, select exampleFile\_2\_7.jar, then click OK.}
-{\bf Note:} Should you want to reload the example alignment or load your own
+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
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
-preferences tab, type in the URL of the sequence you want to load. This
-file will load during the start up process.
+preferences tab, type in the URL of the sequence you want to load.
+
+
As the jalview.jnlp file launches Jalview on your desktop, you
may want to move this from the downloads folder to another folder.
-Opening from this file will allow Jalview to be launched offline.
+Opening from the jnlp file will allow Jalview to be launched offline.
-{\bf Help launching Jalview is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
+{\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}.}
+ }
\subsection{Getting Help}
\label{gettinghelp}
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}.
+ [Fn] key with F2} function
+ [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}
}}
Jalview has two navigation and editing modes: {\bf normal} mode (where editing
and navigation are via the mouse) and the {\bf cursor} mode (where editing and
navigation are via the keyboard).
-The {\bf F2 key} is used to switch between these two modes. With a Mac often
-need to type function {\bf Fn key and F2}, as button is often assigned to
-screen brightness. Jalview always starts up in {\bf normal mode}.
+The {\bf F2 key} is used to switch between these two modes. With a Mac, the key
+combination {\bf Fn key and F2} is needed, as button is
+often assigned to screen brightness. Jalview always starts up in normal mode.
\exstep{Load an example alignment from its URL
(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} dialog
box.
-(The URL should be stored in its history and clicking on the {\sl down arrow} is
-an easy way to access it.)}
+(The URL should be stored in its history and clicking on the {\sl down arrow}
+on the dialog box is an easy way to access it.)}
\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
\exstep{Find the Overview Window, {\sl Views
$\Rightarrow$ Overview Window} and open it. Move around the
alignment by clicking and dragging the red box in the overview window.}
-\exstep{Return to the alignment window. Look at the status bar (lower left hand
-corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
+\exstep{Return to the alignment window, look at the status bar (lower left
+hand corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
sequence and residue under the cursor.}
-\exstep{Press [F2] key (or [Fn]/[F2] on Mac) to enter {\bf Cursor mode}. Use
+\exstep{Press [F2] key, or [Fn]-[F2] on Mac, to enter Cursor mode. Use
the direction keys to move the cursor around the alignment.}
\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
two different positions if gaps are inserted into the sequence. Move to sequence 5,
-column 13 by typing {\bf 1 3 , 5 [RETURN]}.}
+column 13 by typing {\bf 1 3 , 5} [RETURN].}
{\bf Note:} To view Jalview's comprehensive on-line help documentations select
-Help on desktop menu, clicking on Documentation will open a Documentation
-window. Select topic from the navigation panel on the left hand side or use the
+{\sl Help} in desktop menu, clicking on {\sl Documentation} will open a
+Documentation window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words.
-{\bf Help navigating is available in videos on the Getting Started page
-of 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}
\subsection{From a File}
Jalview can read sequence alignments from a sequence alignment file. This is a
-text file, not a word processor document. For entering sequences from a
+text file, {\bf not} a word processor document. For entering sequences from a
wordprocessor document see Cut and Paste (Section \ref{cutpaste}) below. Select
{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main
menu (Figure \ref{loadfile}). You will then get a file selection window where
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]
\label{fetchseq}
Jalview can retrieve sequences and sequence alignments from the public databases
housed at the European Bioinformatics Institute, including Uniprot, Pfam, Rfam
-and the PDB, as well as any DAS sequence server registered at the configured DAS
-registry. Jalview's sequence fetching capabilities allow you to avoid having to
+and the PDB. Jalview's sequence fetching capabilities allow you to avoid having to
manually locate and save sequences from a web page before loading them into
Jalview. It also allows Jalview to gather additional metadata provided by the
source, such as annotation and database cross-references.
press OK. Jalview will then attempt to retrieve them from the chosen database.
Example queries are provided for some databases to test that a source is
operational, and can also be used as a guide for the type of accession numbers
-understood by the source.\footnote{Most DAS sources support {\em range queries}
-that can be used to download just a particular range from a sequence database
-record.}
+understood by the source.
% [fig 9]
\begin{figure}[htbp]
\begin{center}
\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box.
-Click OK to load the alignment.}
+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.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and {\bf save} the file to your desktop.
+your web browser and save the file to your desktop.
Open the file you have just saved in Jalview by selecting {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu and
selecting this file.
-Click OK to load.}
+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.
-Test the differences
+(ii) Test the differences
between (a) dragging the sequence onto the Jalview desktop and (b)
dragging the sequence onto an existing alignment window.
-(ii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
+(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.)
+download directory and open it in a text editor.)}
-(iii) Open the alignment.fa file using text editor. Copy the sequence text from the
-file into the clipboard and paste it into the desktop
-background by right-clicking and selecting Paste to new alignment option.
+\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 the {\sl Paste to New Window} menu
+option.
-(iv) In the text editor, copy the sequence text from
+(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). In the Desktop menu, select {\sl File
+$\Rightarrow$ Copy} menu option).
+
+(iii) In the Desktop menu, select {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
Paste} text box menu option. Click {\sl New Window} and the alignment will be
loaded.}
-\exstep{{\bf Loading sequences from Public Database:} Select {\sl File
-$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
-called New Sequence Fetcher.
-Press database selection button (top of the dialog box), this opens
-another window called Select Database Retrieval Source showing all the database
-sources.
-
-Select the {\bf PFAM seed} database and click OK, then enter the accession
-number {\bf PF03460} and click OK. An alignment of about 174 sequences should
-load. These can be viewed using the Overview window accessible from {\sl View
+
+\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
+$\Rightarrow$ Fetch Sequence(s)...} from the Desktop. The {\sl Select Database
+Retrieval Source} dialog will open showing all the database sources. Select the
+{\bf PFAM seed} database and click {\sl OK}.
+
+(ii)Once a source has been selected, 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 Help loading sequences is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
-}
+{\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 program can read Jalview files. The {\sl File
-$\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
-other documents or web servers.
+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.
+\exstep{Launch Jalview or use close all windows.
Load the ferredoxin
-alignment from PFAM (seed) data base using the PFAM seed accession number
-PF03460 (see Exercise \ref{load}). } \exstep{
+alignment from {\bf PFAM (seed)} data base using the PFAM seed accession number
+{\bf PF03460} (see Exercise \ref{load}). } \exstep{
Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
location into which to save the alignment and select your preferred format. All
formats except {\sl Jalview } jvp can be viewed in a normal text editor (e.g.
Notepad) or in a web browser.
-Enter a file name and click {\sl Save}.
-
-Check this file by closing all windows and opening it with Jalview, or by
+Enter a file name and click {\sl Save}.}
+\exstep{Check this file by closing all windows and opening it with Jalview, or by
browsing to it with your web browser.}
-\exstep{ Repeat the previous step saving the files in different file formats.}
+\exstep{Repeat the previous steps saving the files in different file formats.}
\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}.
Select and copy this alignment to the clipboard using the textbox menu options
{\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}.
and scroll red box to any part of the alignment.
Select {\sl File
$\Rightarrow$ Save Project} from the main menu and save the project in a
-suitable folder.
+suitable folder.}
-Close all windows and then load the project {\sl via} the {\sl File
+\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 Help saving sequences is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
+{\bf See the video at: \url{http://www.jalview.org/Help/Getting-Started}.}
+}
\chapter{Selecting and Editing Sequences }
{\bf To clear (unselect) the selection press the [ESC] (escape) 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. A dashed red box appears around the selected region (Figure \ref{select}).
+To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button.
+A dashed red box appears around the selected region (Figure \ref{select}).
%[fig 12]
\begin{figure}[htbp]
$\Rightarrow$ 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 (PF03460 from PFAM seed database).
-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
+
+Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).
+}
+\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 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{ To selecting arbitrary regions in alignment, place the mouse at the top
-left corner of the region you wish to select. Press and hold the mouse button.
-Drag the mouse to the bottom right corner of the chosen region and release the
-mouse button and a dashed red box appears around the selected region}
-\exstep{Enter Cursor mode using [F2] (or [Fn]-F2 for Macs).
+\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]}.
Press {\bf Q} to mark this position.
Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
-to complete the selection. Note to clear the selection press the {\bf[ESC]}
+to complete the selection. Note to clear the selection press the [ESC]
key.}
-\exstep{To create a {\bf group} from the selected the region, click the
+\exstep{To create a group from the selected the region, click the
right mouse button when mouse is on the selection, this opens a
-pop-up menu in the alignment window.
+context menu in the alignment window.
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
-} menu and select `Percentage Identity'.
+} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
-to include newly selected sequences, and the `Percentage Identity' colouring changes. }
+to include newly selected sequences, and the Percentage Identity colouring changes. }
\exstep{ Another way to resize the group is by using the mouse to click and drag
the right-hand edge of the selected group.}
-\exstep{The current selection can be {\bf exported} and saved by right clicking
-on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
-output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
+\exstep{The current selection can be exported and saved by right clicking the
+mouse when on the text area to open the Sequence ID context menu. Follow the
+menus and pick an output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
\ldots} submenu.
}
-\exstep{In the alignment output window, try manually editing the alignment,
-importing group into a new alignment window by clicking the [New Window] button to import the
-file into a new alignment window.}
-{\bf Additional help is available from videos 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.
}
\end{figure}
\exercise{Reordering the Alignment}{
-\exstep{Close all windows in Jalview from desktop. Load the ferredoxin alignment (e.g.the
-PFAM domain PF03460 from PFAM seed).
+\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
arrow keys to alter the sequence's position in the alignment. (Note that
this will not work in cursor mode)}
\exstep{To select and move multiple
-sequences, use hold [SHIFT] and [CTRL], and select two sequences separated by
-one or more un-selected sequences. Note how multiple sequences are grouped
-together when they are re-ordered using the up and down arrow keys.}
-{\bf Additional help is available from videos on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}}
+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 See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+}
\section{Hiding Regions}
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
\exercise{Hiding and Revealing Regions}{
-\exstep{Close all windows, open the PFAM accession PF03460. Select a
-contiguous set of sequences by clicking and dragging on the sequence ID panel.
-Right click on the selected sequence IDs to bring up the sequence ID pop-up
+\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.
+Right click on the selected sequence IDs to bring up the sequence ID context
menu, select {\sl Hide Sequences}.
}
\exstep{
All Sequences.}) }
\exstep{
Repeat the process but use a non-contiguous set of sequences. Note that when
-multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
+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.}
-\exstep{Select a region of the alignment, then add in some additional columns to
-the selection, and experiment with the `Hide all but selected region' function
-in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
-\exstep{Select some sequences and pick one to represent the rest by hovering
-the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
-clicking and then select {\sl (Sequence ID name) $\Rightarrow$ Represent group
+\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
+but selected region} option in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
+the mouse over this sequence. Bring up the Sequence ID context menu by right
+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 pop-up menu select Reveal All.}
-{\bf Additional help is available from videos on the Jalview
-website at \url{http://www.jalview.org/training/Training-Videos}}}
+Sequence ID and in the context menu select {\sl Reveal All}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+}
\begin{figure}[htb]
\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
% % 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
+under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
+press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
+or [SHIFT]-[SPACE] (both keys held down together).
+
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
+have everything unselected by pressing ESC. The gap under the cursor will be
+removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
+will be deleted up to the number specified. To delete gaps from all sequences of
+a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
+together). Note that the deletion will only occur if the gaps are in the same
+columns in all sequences in the selected group, and those columns are to the
+right of the selected residue.
+
+\newpage
+
\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
-Remember to use [CTRL]+Z to undo an edit, or the {\sl File $\Rightarrow$
+
+{\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
want to start again.
-If you are using OSX, and a key combination - such as [CTRL]+A - does
- not work, then try pressing the [CMD] key instead of [CTRL].
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
ferredoxin alignment from PF03460.}
\exstep{ Select the first 7 sequences, and press H to hide them (or right click
-on the sequence IDs to open the sequence ID pop-up menu, and select {\sl Hide
+on the sequence IDs to open the sequence ID context menu, and select {\sl Hide
Sequences}).}
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
-the right so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
+the right so the initial residue A lies at column 57 using the $\Rightarrow$
+key.}
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
O80429\_MAIZE
Insert another gap at column 47 in all sequences in the same way.}
\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
-inserting two additional gaps after the gap at column 47: First press [ESC] to
+inserting two additional gaps after the gap at column 47. First press [ESC] to
clear the selection, then hold [SHIFT] and click and drag on the G and move it
two columns to the right.}
\exstep{ Now complete the
-alignment of FER1\_SPIOL with a {\bf locked edit} by pressing [ESC] and select
+alignment of FER1\_SPIOL with a locked edit by pressing [ESC] and select
columns 47 to 57 of the FER1\_SPIOL row. Move the mouse onto the G at column 50,
hold [SHIFT] and drag the G in column 47 of FER1\_SPIOL to the left by one
column to insert a gap at column 57.}
column 44, and insert 4 gaps at column 47 (after AAPM).}
\exstep{ Hold [SHIFT] and drag the I at column 39 of FER1\_MAIZE 2 columns to the
-right. Remove the gap at FER1\_MAIZE column 49 by [SHIFT]+click and drag left by
+right. Remove the gap at FER1\_MAIZE column 49 by [SHIFT]-click and drag left by
one column. Press [ESC] to clear the selection, and then insert three gaps in
FER1\_MAIZE at column 47 by holding [SHIFT] and click and drag the S in FER1\_MAIZE to the right by three columns. Finally,
remove the gap in O80429\_MAIZE at column 56 using [SHIFT]-drag to the left on
\exstep{ Use the
{\sl Edit $\Rightarrow$ Undo Edit} and {\sl Edit $\Rightarrow$ Redo Edit} menu
-option, or their keyboard shortcuts ([CTRL]+Z and [CTRL]+Y) to step
+option, or their keyboard shortcuts ([CTRL]-Z and [CTRL]-Y) to step
backwards and replay the edits you have made.}
}
-\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
-under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
-press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
-or [SHIFT]-[SPACE] (both keys held down together).
-
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
-have everything unselected by pressing ESC. The gap under the cursor will be
-removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
-will be deleted up to the number specified. To delete gaps from all sequences of
-a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
-together). Note that the deletion will only occur if the gaps are in the same
-columns in all sequences in the selected group, and those columns are to the
-right of the selected residue.
-
-\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.
\exercise{Keyboard Edits}
-{This continues on from exercise
-\ref{mousealedit}, and recreates the final part of the example ferredoxin
+{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
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
-edited alignment from exercise \ref{mousealedit}. If you continue from the
+edited alignment. If you continue from the
previous exercise, first right click on the sequence ID panel and select
{\sl Reveal All}. Enter cursor mode by pressing [F2].}
% TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
column 38.
Press {\sl 34C [BACKSPACE] 38C 2 [SPACE]}. Delete three gaps at column 44 and
insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are
-now aligned.}
-}
+now aligned.}}
\chapter{Colouring Sequences and Figure Generation}
\label{colouringfigures}
\subsection{Colouring a Group or Selection}
Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above,
- after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected.
+ after first ensuring that the {\sl Apply Colour To All Groups} flag is {\bf
+ not} selected.
This must be turned {\sl off} specifically as it is {\sl on} by default.
When unticked, selections from the Colours menu will only change the colour for residues in the current selection,
or the alignment view's ``background colourscheme'' when no selection exists.
} \parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
-\exercise{Colouring Alignments}{
-\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected
-in View sequence alignment menu.
- This must be turned {\sl off} specifically as it is {\sl on} by default.}
-\exstep{
-Open a sequence alignment, for example the PFAM domain PF03460 in PFAM seed.
-Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
-}
-\exstep{
-Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group
+\exercise{Colouring Alignments}{
+\label{color}
+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.
+Note that some colour schemes do not colour all residues.}
+\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group
of around 4 similar sequences. Use the context menu (right click on the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
-colouring schemes like Blosum62 are based on the group being coloured, not the
-whole alignment (this also explains the colouring changes observed in exercise
-\ref{exselect} during the group selection step).
-}
-\exstep{
-Keeping the same selection as before, colour the complete alignment except
+colouring schemes like Blosum62 are based on the selected group,
+not the whole alignment (this also explains the colouring changes observed in exercise
+\ref{exselect} during the group selection step).}
+\exstep{Keeping the same selection as before, colour the complete alignment except
the group using {\sl Colour $\Rightarrow$ Taylor}.
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
-Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
-}
+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 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}).
+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]
\exercise{User Defined Colour Schemes}{
-\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.
-}
-\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.
-}
-\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.
-}
-\exstep{
-The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
-}
-}
+\exstep{Load a sequence alignment. 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 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 See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}} }
\section{Formatting and Graphics Output}
\label{layoutandoutput}
Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
sequence ID format and so on. }
-\exstep{Hide all the annotation rows by selecting {\sl Annotations $\Rightarrow$
+\exstep{Hide all the annotation rows by toggling {\sl Annotations $\Rightarrow$
Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} \exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
-annotation row labels to bring up the pop-up context menu, then select {\sl
-Hide This Row}. Bring up the pop-up context menu again and select {\sl
+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} below.}
-\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label -
+\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{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 the mouse up or down.}
+by clicking and dragging this icon up or down.}
}
\subsection{Graphical Output}
For submission of alignment figures to journals, please use EPS\footnote{If the journal complains, {\em insist}.}.
}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
+
\exercise{Graphical Output}{
\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}.
Customise it how you wish but leave it unwrapped.
alignment window but {\bf annotations are not exported}).}
\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option.
Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in.
-Notice that the image is a bitmap and it becomes pixelated very quickly.
+Notice that the image is a bitmap and it becomes pixelated when zoomed.
(Note that the {\bf annotation lines are included} in the image.)}
\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image
$\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
Preview (Mac OS X). Zoom in and note that the image has near-infinite
-resolution.} }
+resolution.}
+}
-\chapter{Features and Annotation}
-\label{annotation}
-\section{Features and Annotation}
-\label{featannot}
-Features and annotations are additional information that is overlaid on the sequences and the alignment. Generally speaking, annotations are associated with columns in the alignment. Features are associated with specific residues in the sequence.
+\newpage
+
+\section{Summary - the rest of the manual}
-Annotations are shown below the alignment in the annotation panel, and often reflect properties of the alignment as a whole. The Conservation, Consensus and Quality scores are examples of dynamic annotation, so as the alignment changes, they change along with it. Conversely, sequence features are properties of the individual sequences, so they do not change with the alignment, but are shown mapped on to specific residues within the alignment.
+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}
+Annotations and features are additional information that is
+overlaid on the sequences and the alignment.
+Generally speaking, annotations reflect properties of the alignment as a
+whole, often associated
+with columns in the alignment. Features are often associated with specific
+residues in the sequence.
+
+Annotations are shown below the alignment in the annotation panel, the
+properties are often based on the alignment.
+Conversely, sequence features are properties of the individual sequences, so they do not change with the alignment,
+but are shown mapped on to specific residues within the alignment.
Features and annotation can be interactively created, or retrieved from external
-data sources. DAS (the Distributed Annotation System) is the primary source of
-sequence features, whilst webservices like JNet (see \ref{jpred} above) can be used to analyse a
+data sources. Webservices like JNet (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}
+\label{annotationintro}
+Jalview automatically calculates several quantitative alignment annotations
+which are displayed as histograms below the multiple sequence alignment columns.
+Conservation, quality and consensus scores are examples of dynamic
+annotation, so as the alignment changes, they change along with it.
+The scores can be used in the hybrid colouring options to shade the alignments.
+Mousing over a conservation histogram reveals a tooltip with more information.
+
+These annotations can be hidden and deleted via the context menu linked to the
+annotation row; but they are only created on loading an alignment. If they are
+deleted then the alignment should be saved and then reloaded to restore them.
+Jalview provides a toggle to autocalculate a consensus sequence upon editing. This is normally selected by default, but can be turned off for
+large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
+Consensus} menu option if the interface is too slow.
+
+\subsubsection{Conservation Annotation}
+
+Alignment conservation annotation is quantitative numerical index reflecting the
+conservation of the physico-chemical properties for each column of the alignment.
+The calculation is based on AMAS method of multiple sequence alignment analysis (Livingstone C.D. and Barton G.J. (1993) CABIOS Vol. 9 No. 6 p745-756),
+with identities scoring highest, and amino acids with substitutions in the same physico-chemical class have next highest score.
+The score for each column is shown below the histogram.
+The conserved columns with a score of 11 are indicated by '*'.
+Columns with a score of 10 have mutations but all properties are conserved are marked with a '+'.
+
+\subsubsection{Consensus Annotation}
+
+Alignment consensus annotation reflects the percentage of the different residue
+per column. By default this calculation includes gaps in columns, gaps can be ignored via the Consensus label context
+menu to the left of the consensus bar chart.
+The consensus histogram can be overlaid
+with a sequence logo that reflects the symbol distribution at each column of
+the alignment. Right click on the Consensus annotation row and select the {\sl Show
+Logo} option to display the Consensus profile for the group or alignment.
+Sequence logos can be enabled by default for all new alignments {\sl via} the
+Visual tab in the Jalview desktop's preferences dialog box.
+
+\subsubsection{Quality Annotation}
+
+Alignment quality annotation is an ad-hoc measure of the likelihood of observing
+the mutations (if any) in a particular column of the alignment. The quality score is calculated for each column in an alignment by summing,
+for all mutations, the ratio of the two BLOSUM 62 scores for a mutation pair and each residue's conserved BLOSUM62 score (which is higher).
+This value is normalised for each column, and then plotted on a scale from 0 to 1.
+
+\subsubsection{Group Associated Annotation}
+\label{groupassocannotation}
+Group associated consensus and conservation annotation rows reflect the
+sequence variation within a particular group. Their calculation is enabled
+by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
+the {\sl Annotation $\Rightarrow$ Autocalculated Annotation } submenu of the
+alignment window.
+
+\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 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 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.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=1.3in]{images/annots1.pdf}
+\includegraphics[width=2in]{images/annots2.pdf}
+\caption{{\bf Creating a new annotation row.} Annotation rows can be reordered by dragging them to the desired place.}
+\label{newannotrow}
+\end{center}
+\end{figure}
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2in]{images/annots3.pdf}
+\includegraphics[width=2in]{images/annots4.pdf}
+\includegraphics[width=2in]{images/annots5.pdf}
+\caption{{\bf Creating a new annotation.} Annotations are created from a selection on the annotation row and can be coloured as desired.}
+\label{newannot}
+\end{center}
+\end{figure}
+
+\subsection{Automated Annotation of Alignments and Groups}
+
+On loading a sequence alignment, Jalview will normally\footnote{Automatic
+annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
+$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
+rows which are shown below the alignment. For nucleotide sequence alignments,
+only an alignment consensus row will be shown, but for amino acid sequences,
+alignment quality (based on BLOSUM 62) and physicochemical conservation will
+also be shown. Conservation is calculated according to Livingstone and
+Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the
+Hierarchical Analysis of Residue Conservation." } Livingstone C.D. and Barton
+G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
+Consensus is the modal residue (or {\tt +} where there is an equal top residue).
+The inclusion of gaps in the consensus calculation can be toggled by
+right-clicking on the Consensus label and selecting {\sl Ignore Gaps in
+Consensus} from the pop-up context menu located with consensus annotation row.
+Quality is a measure of the inverse likelihood of unfavourable mutations in the alignment. Further details on these
+calculations can be found in the on-line documentation.
+
+
+\exercise{Annotating Alignments}{
+\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 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.
+}
+\exstep{
+Navigate to column 97. Move down and on the new annotation row called
+``Iron binding site, select column 97.
+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 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.
+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.
+{\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.}
+\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.}
+}
+\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
+SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
+annotation. }
+
+
\section{Importing Features from Databases}
\label{featuresfromdb}
-Jalview supports feature retrieval from public databases either directly or {\sl
-via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}).
+Jalview supports feature retrieval from public databases.
It includes built in parsers for Uniprot and ENA (or EMBL) records retrieved
from the EBI. Sequences retrieved from these sources using the sequence fetcher (see
Section \ref{fetchseq}) will already possess features.
Sequence Fetcher} has access to. This function is accessed from the {\sl
Webservice $\Rightarrow$ Fetch DB References} sub-menu in the Alignment
window. This menu allows you to query either the set of {\sl Standard
-Databases}, which includes EMBL, Uniprot, the PDB, and the currently selected
-DAS sequence sources, or just a specific datasource from one of the submenus.
+Databases}, which includes EMBL, Uniprot, the PDB, or just a specific datasource from one of the submenus.
When one of the entries from this menu is selected, Jalview will use the ID
string from each sequence in the alignment or in the currently selected set to
retrieve records from the external source. Any sequences that are retrieved are
the database did not exactly contain the sequence given in the alignment (the
{\sl ``Sequence not 100\% match'' dialog box}).
-\exercise{Retrieving Database References}{
-\exstep{Load the example alignment at http://www.jalview.org/tutorial/alignment.fa}
-\exstep{Verify that there are no database references for the sequences by first
-checking that the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show
-Database Refs} option is selected, and then mousing over each sequence's ID.}
-\exstep{Use the {\sl Webservice $\Rightarrow$ Fetch DB References} menu option to retrieve database IDs for the sequences.}
-\exstep{Examine the tooltips for each sequence in the alignment as the retrieval progresses - note the appearance of new database references.}
-\exstep{Once the process has finished, save the alignment as a Jalview Project.}
-\exstep{Now close all the windows and open the project again, and verify that the database references and sequence features are still present on the alignment}
-
-\exstep{View the {\sl Sequence details \ldots} report for the FER1\_SPIOL sequence and for the whole alignment. Which sequences have web links associated with them ?}
-
-}
-
-\subsection{Retrieving Features {\sl via} DAS}
-\label{dasfretrieval}
-Jalview includes a client to retrieve features from DAS annotation servers. To
-retrieve features, select {\sl View $\Rightarrow$ Feature Settings\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab in the Sequence Feature Settings Window (Figure \ref{das}). A list of DAS sources compiled from the currently configured DAS registry\footnote{By default, this will be the major public DAS server registry maintained by the Sanger Institute: http://www.dasregistry.org} is shown in the left hand pane. Highlighting an entry on the left brings up information about that source in the right hand panel.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.5in]{images/das1.pdf}
-\includegraphics[width=2.5in]{images/das2.pdf}
-\caption{{\bf Retrieving DAS annotations.} DAS features are retrieved using the {\sl DAS Settings} tab (left) and their display customised using the {\sl Feature Settings} tab (right).}
-\label{das}
-\end{center}
-\end{figure}
-
-Select appropriate DAS sources as required then click on {\sl Fetch DAS
-Features}. If you know of additional sources not listed in the configured
-registry, then you may add them with the {\sl Add Local Source} button. Use
-the {\sl Authority},{\sl Type}, and {\sl Label} filters to restrict the list
-of sources to just those that will return features for the sequences in the
-alignment.
-
-Following DAS feature retrieval, the {\sl Feature Settings} panel takes on a
-slightly different appearance (Figure \ref{das} (right)). Each data source is
-listed and groups of features from one data source can be selected/deselected
-by checking the labelled box at the top of the panel.
-
-\exercise{Retrieving Features with DAS}{
-\label{dasfeatretrexcercise}
-\exstep{Load the alignment at
-\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
-$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
-the {\sl DAS Settings} tab. A long list of available DAS sources is listed.
-Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click.
-A window may prompt whether you wish Jalview to fetch DAS features. Click {\sl
-Yes}.
-Jalview will start retrieving features. As features become available they will be mapped onto the alignment. }
-\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button.
-Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip.
-Close the Sequence Feature Settings window. }
-\exstep{Move the mouse over the sequence ID panel.
-Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
-\exstep{Search through the alignment to find a feature with a link symbol next to it.
-Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
-% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
-
-\exstep{
-Select {\sl View $\Rightarrow$ Feature Settings\ldots} to reopen the Feature Settings window. All the loaded feature types should now be displayed. Those at the top of the list are drawn on top of those below, obscuring them in the alignment view where they overlap. Move the feature settings window so that the alignment is visible and uncheck some of the feature types by clicking the tick box in the display column. Observe how the alignment display changes. Note that unselected feature types do not appear in the tool tip.
-}
-\exstep{Reorder the features by dragging feature types up and down the order in the Feature Settings panel. e.g. Click on {\sl CHAIN} then move the mouse downwards to drag it below {\sl DOMAIN}. Note that {\sl DOMAIN} is now shown on top of {\sl CHAIN} in the alignment window. Drag {\sl METAL} to the top of the list. Observe how the cysteine residues are now highlighted as they have a {\sl METAL} feature associated with them.
-}
-
-\exstep{Press the {\sl Optimise Order} button. The features will be ordered according to increasing length, placing features that annotate shorter regions of sequence higher on the display stack.}
-
-\exstep{Select {\sl File $\Rightarrow$ Export Features\ldots} from the Alignment window. You can choose to export the retrieved features as a GFF file, or Jalview's own Features format.
-% TODO: describe working with features files and GFF
-}
-}
\subsubsection{The Fetch Uniprot IDs Dialog Box}
\label{discoveruniprotids}
If any sources are selected which refer to Uniprot coordinates as their reference system,
-then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing OK instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Service $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}. If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record to ensure that features retrieved from the DAS source are rendered at the correct position.
+then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing OK instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Service $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}.
+If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record.
\subsubsection{Rate of Feature Retrieval}
Feature retrieval can take some time if a large number of sources is selected and if the alignment
-contains a large number of sequences. This is because Jalview only queries a particular DAS source with one sequence at a time, to avoid overloading it. As features are retrieved, they are immediately added to the current alignment view. The retrieved features are shown on the sequence and can be customised as described previously.
+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{Colouring Features by Score or Description
% }
\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
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
appropriate box. Click on the Feature Colour bar to change the colour if
-desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at 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.
+desired, add a short description (``One of four Iron binding Cysteines") and
+press {\sl OK}. The features will then appear on the sequences. } \exstep{Roll
+the mouse cursor over the new features.
+Note that the position given in the tool tip is the residue number, not the column number.
+To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at column 95.
+Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
}
\exstep{
-Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
+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
this so that you can see the features you have just created. Click the check
box for ``Iron binding site" under {\sl Display} and note that display of this
feature type is now turned off. Click it again and note that the features are
-now displayed. Close the sequence feature settings box by clicking OK or
-Cancel.} }
-
-\subsection{Creating User Defined Annotation}
-
-Annotations are properties that apply to the alignment as a whole and are visualized on rows in the annotation panel.
-To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}). A dialogue box appears. Enter the label to use for this row and a new row will appear.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=1.3in]{images/annots1.pdf}
-\includegraphics[width=2in]{images/annots2.pdf}
-\caption{{\bf Creating a new annotation row.} Annotation rows can be reordered by dragging them to the desired place.}
-\label{newannotrow}
-\end{center}
-\end{figure}
-
-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, 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.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2in]{images/annots3.pdf}
-\includegraphics[width=2in]{images/annots4.pdf}
-\includegraphics[width=2in]{images/annots5.pdf}
-\caption{{\bf Creating a new annotation.} Annotations are created from a selection on the annotation row and can be coloured as desired.}
-\label{newannot}
-\end{center}
-\end{figure}
-
-\exercise{Annotating Alignments}{
-\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 appear asking for {\sl Label for annotation}.
-Enter ``Iron binding site" and click OK. A new, empty, row appears.
-}
-\exstep{
-Navigate to column 97. Move down and on the new annotation row called
-``Iron binding site, select column 97.
-Right click at this selection and select {\sl Label} from the context menu.
-Enter ``Fe" in the box and click OK. Right-click on the selection again and select {\sl Colour}.
-Choose a colour from the colour chooser dialogue
-and click OK. Press [ESC] to remove the selection.
-}
-\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
- context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the
- sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet
- arrow.
-}
-\exstep{Right click on the title text of annotation row that you just created.
-Select {\sl Export Annotation} and, in the {\bf Export Annotation} dialog box that will open, select the Jalview format and click
-the [To Textbox] button.
-
-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{Try to add an additional helix somewhere along the row by editing the file and
-re-importing it.
-{\sl Hint: Use the {\bf Export Annotation} function to view what helix annotation looks like in
-a Jalview annotation file.}}
-\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
-function to export all the alignment's annotation to a file.}
-\exstep{Open the exported annotation in a text editor, and use the {\bf Annotation File Format}
-documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
-they appear as several lines on a single line graph.
-{\sl Hint: You need to change the style of annotation row in the first field of the annotation
-row entry in the file, and create an annotation row grouping to overlay the three quantitative
-annotation rows.}
-}
-\label{viewannotfileex}\exstep{Recover or recreate the secondary structure
-prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export
-Annotation} function to view the Jnet secondary structure prediction annotation row. Note the
-{\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the
-annotation. } }
+now displayed. Close the sequence feature settings box by clicking {\sl OK} or
+{\sl Cancel}.} }
\chapter{Multiple Sequence Alignment}
\label{msaservices}
Sequences can be aligned using a range of algorithms provided by JABA web
-services. These include ClustalW\footnote{{\sl ``CLUSTAL W: improving the
-sensitivity of progressive multiple sequence alignment through sequence
+services, including ClustalW\footnote{{\sl ``CLUSTAL W:
+improving the sensitivity of progressive multiple sequence alignment through sequence
weighting, position specific gap penalties and weight matrix choice."} Thompson
JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic Acids Research} {\bf 22},
4673-80}, Muscle\footnote{{\sl ``MUSCLE: a multiple sequence alignment method
McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) {\sl Molecular
Systems Biology} {\bf 7} 539
\href{http://dx.doi.org/10.1038/msb.2011.75}{doi:10.1038/msb.2011.75}} Of these,
-T-COFFEE is the slowest, but also the most accurate. ClustalW is historically
-the most widely used. Muscle is faster than ClustalW and probably the most
-accurate for smaller alignments and MAFFT is probably the best for large
-alignments, however {\bf Clustal Omega}, which was released in 2011, is
-arguably the fastest and most accurate tool for protein multiple alignment.
-
+T-COFFEE is slow but the 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.
To run an alignment web service, select the appropriate method from the {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ \ldots} submenu (Figure
default settings, use one of the available presets, or customise the parameters
with the `{\sl Edit and Run ..}' dialog box. Once the job is submitted, a
progress window will appear giving information about the job and any errors that
-occur. After successful completion of the job, a new window is opened with the
-results, in this case an alignment. By default, the new alignment will be
-ordered in the same way as the input sequences; however, many alignment programs
-re-order the input to place homologous sequences close together. This ordering
-can be recovered using the `Original ordering' entry within the {\sl Calculate
-$\Rightarrow$ Sort } sub menu.
+occur. After successful completion of the job, a new alignment window is opened
+with the results, in this case an alignment. By default, the new alignment will be
+ordered in the same way as the input sequences. Note: many alignment
+programs re-order the input during their analysis and place homologous
+sequences close together, the MSA algorithm ordering can be recovered
+using the `Algorithm ordering' entry within the {\sl Calculate $\Rightarrow$
+Sort } sub menu.
+
+\subsubsection{Realignment}
+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.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{Realignment}
-
-The re-alignment option is currently only supported by ClustalW and Clustal
-Omega. When performing a re-alignment, Jalview submits the current selection to
-the alignment service complete with any existing gaps. This approach is useful
-when one wishes to align additional sequences to an existing alignment without
-any further optimisation to the existing alignment. The re-alignment service
-provided by ClustalW in this case is effectively a simple form of profile
-alignment.
-
\subsubsection{Alignments of Sequences that include Hidden Regions}
-
If the view or selected region that is submitted for alignment contains hidden
regions, then {\bf only the visible sequences will be submitted to the service}.
Furthermore, each contiguous segment of sequences will be aligned independently
columns can be used to preserve existing parts of an alignment whilst the
visible parts are locally refined.
-\exercise{Multiple Sequence Alignment}{
-\exstep{ Close all windows and open the alignment at {\sf
-http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
-Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}.
-A window will open giving the job status. After a short time, a second window will open
- with the results of the alignment.}
- \exstep{Return to the first sequence alignment window by clicking on
- the window, and repeat using Clustal and MAFFT (from the {\sl Web
- Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and
- you should notice small differences. }
-\exstep{Select the last three sequences in the MAFFT alignment, and de-align them
-with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect them and then
-submit the view for re-alignment with Clustal.}
-\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment.
-Once the Clustal re-alignment has completed, compare the results of re-alignment of the
-three sequences with their alignment in the original MAFFT result.}
-\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them.
-Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to
-submit the visible portion of the alignment to MAFFT. When the web service job pane appears,
-note that there are now two alignment job status panes shown in the window.}
-\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible
-region in the result with the corresponding region of the original alignment. If you wish,
-select and hide a few more columns in the N-terminal region, and submit the alignment to the
-service again and explore the effect of local alignment on the non-homologous parts of the
-N-terminal region.}
-}
-
\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:
\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
service can also be accessed, by right clicking the button and selecting a URL
from the pop-up menu that will open.
+\exercise{Multiple Sequence Alignment}{
+\exstep{ Close all windows and open the alignment at {\sf
+http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
+Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}.
+A window will open giving the job status. After a short time, a second window will open
+ with the results of the alignment.}
+ \exstep{Return to the first sequence alignment window by clicking on
+ the window, and repeat using {\sl ClustalO} (Omega) and {\sl MAFFT}, from the
+ {\sl Web Service $\Rightarrow$ Alignment} menu, using the same initial
+ alignment.
+ Compare them and you should notice small differences. }
+\exstep{Select the last three sequences in the MAFFT alignment, and de-align them
+with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
+sequences. Then submit this view for re-alignment with {\sl ClustalO}.}
+\exstep{Return to the alignment window in section (c), use [CTRL]-Z (undo) to
+recover the alignment of the last three sequences in this MAFFT alignment.
+Once the ClustalO re-alignment has completed, compare the results of
+re-alignment of the three sequences with their alignment in the original MAFFT result.}
+\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them,
+by right clicking the mouse to bring up context menu.
+Select {\sl Web Service $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to
+submit the visible portion of the alignment to MAFFT. When the web service job pane appears,
+note that there are now two alignment job status panes shown in the window.}
+\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible
+region in the result with the corresponding region of the original alignment.}
+\exstep {If you wish,
+select and hide a few more columns in the N-terminal region, and submit the alignment to the
+service again and explore the effect of local alignment on the non-homologous parts of the
+N-terminal region.}
+{\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
+
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2.5in]{images/clustalwparamdetail.pdf}
analytical methods are `built-in', these are accessed from the {\sl Calculate}
alignment window menu. Computationally intensive analyses are run outside
Jalview {\sl via} web services - these are typically accessed {\sl via} the {\sl
-Web Service} menu, and described in \ref{jvwebservices} and subsequent sections.
+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.
\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
-the calculation finishes, a 3D viewer displays the each sequence as a point in
+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.
Note: The calculation is computationally expensive, and may fail for very large
\subsubsection{What is PCA?}
Principal components analysis is a technique for examining the structure of
complex data sets. The components are a set of dimensions formed from the
-measured values in the data set, and the principle component is the one with the
+measured values in the data set, and the principal component is the one with the
greatest magnitude, or length. The sets of measurements that differ the most
-should lie at either end of this principle axis, and the other axes correspond
+should lie at either end of this principal axis, and the other axes correspond
to less extreme patterns of variation in the data set.
In this case, the components are generated by an eigenvector decomposition of
the matrix formed from the sum of pairwise substitution scores at each aligned
\subsubsection{The PCA Viewer}
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principal
Component Analysis} menu option. {\bf PCA requires a selection containing at
least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}).
Each sequence is represented by a small square, coloured by the background
keys or the scroll wheel of the mouse (if available). A tool tip appears if the
cursor is placed over a sequence. Sequences can be selected by clicking on them.
[CTRL]-Click can be used to select multiple sequences.
+
+Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$
+Show Labels} menu option, and the plot background colour changed {\sl via} the
+{\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical
+representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
+the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
+
+\exercise{Principal Component Analysis}
+{ \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.
+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.
+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 See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
+
\begin{figure}[hbtp]
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\end{center}
\end{figure}
-Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$
-Show Labels} menu option, and the plot background colour changed {\sl via} the
-{\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical
-representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
-the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
-\exercise{Principle Component Analysis}{ \exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar} and press [ESC] to clear any selections. Alternatively, select {\sl Select $\Rightarrow$ Undefine Groups} to remove all groups and colourschemes. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
-\exstep{ Click on the tree window. Careful selection of the tree partition
-location will divide the alignment into a number of groups, each of a different
-colour. Note how the colour of the sequence ID label matches both the colour of
-the partitioned tree and the points in the PCA plot.
-} }
\subsubsection{PCA Data Export}
Although the PCA viewer supports export of the current view, the plots produced
} \parbox[c]{3in}{\centerline{
\includegraphics[width=2.5in]{images/pca_vmenu.pdf} }}
-
-\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview
-(Either start with this link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
-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 ``latest official build'' row in the table, go to the
-``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 new tree window will appear.}
-\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
-\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring
-makes it easy to see the differences between the two trees, calculated using
- different methods.} \exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
-Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the alignment for the calculation of trees.
-}
-\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
-
-A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
-
-\exstep{Now select {\sl Edit $\Rightarrow$ Pad Gaps } and try to perform the tree calculation again - this time a new tree should appear.
-
-This demonstrates the use of the {\sl Pad Gaps } editing preference, which ensures that all sequences are the same length after editing. }
-
-}
-
\subsection{Tree Based Conservation Analysis}
\label{treeconsanaly}
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 See the video 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}.
+
+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}.
+
+{\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
+
\exercise{Tree Based Conservation Analysis}{
\label{consanalyexerc}
-\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbour joining tree using BLOSUM62 and use the {\sl Sort
-Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.} \exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
-
-You may find it easier to browse the alignment if you first uncheck the {\sl
-Annotations $\Rightarrow$ Show Annotations} option, and open the Overview Window
-within the View menu to aid navigation.}
-\exstep{Try changing the colourscheme to BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected)}
+\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.}
+\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.}
+
+\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 few exercises. } }
+it is used in the next set of exercises. }
+
+{\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
+
\subsection{Redundancy Removal}
\caption{The Redundancy Removal dialog box opened from the edit menu. Sequences that exceed the current percentage identity threshold and are to be removed are highlighted in black.}
\end{figure}
-\exercise{Remove Redundant Sequences}{
-
-\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
-the alignment window, you may need to deselect groups using Esc key.}
-\exstep{In the Edit menu select Remove Redundancy to open the Redundancy
-threshold selection dialog. Adjust the redundancy threshold value, start
-at 50 and increase the value to 65. Sequences selected will change colour in the Sequence ID panel. Select ``Remove'' to
-remove the sequences that are more than 65\% similar under this alignment.}
-\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
-\exstep{Use the [Undo] button in the Redundancy threshold selection dialog box
-to recover the sequences. Note that the * symbols disappear from the tree display.}
-\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
-}
\subsection{Subdividing the Alignment According to Specific Mutations}
colourschemes can then be used to reveal any associated pattern of sequence
variation across the whole alignment.
-\subsection{Automated Annotation of Alignments and Groups}
-On loading a sequence alignment, Jalview will normally\footnote{Automatic
-annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
-$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
-rows which are shown below the alignment. For nucleotide sequence alignments,
-only an alignment consensus row will be shown, but for amino acid sequences,
-alignment quality (based on BLOSUM 62) and physicochemical conservation will
-also be shown. Conservation is calculated according to Livingstone and
-Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the
-Hierarchical Analysis of Residue Conservation." } Livingstone C.D. and Barton
-G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
-Consensus is the modal residue (or {\tt +} where there is an equal top residue).
-The inclusion of gaps in the consensus calculation can be toggled by
-right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
-Consensus} from the pop-up context menu located with consensus annotation row.
-Quality is a measure of the inverse likelihood of unfavourable mutations in the alignment. Further details on these
-calculations can be found in the on-line documentation.
+% These annotations can be hidden and deleted via the context menu linked to the
+% annotation row; but they are only created on loading an alignment. If they are
+% deleted then the alignment should be saved and then reloaded to restore them.
+% Jalview provides a toggle to autocalculate a consensus sequence upon editing.
+% This is normally selected by default, but can be turned off for large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
+% Consensus} menu option if the interface is too slow.
-These annotations can be hidden and deleted via the context menu linked to the
-annotation row; but they are only created on loading an alignment. If they are
-deleted then the alignment should be saved and then reloaded to restore them.
-Jalview provides a toggle to autocalculate a consensus sequence upon editing. This is normally selected by default, but can be turned off for
-large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
-Consensus} menu option if the interface is too slow.
+% \subsubsection{Group Associated Annotation}
+% \label{groupassocannotation}
+% Group associated consensus and conservation annotation rows reflect the
+% sequence variation within a particular group. Their calculation is enabled
+% by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
+% the {\sl Annotation $\Rightarrow$ Autocalculated Annotation } submenu of the
+% alignment window.
-\subsubsection{Group Associated Annotation}
-\label{groupassocannotation}
-Group associated consensus and conservation annotation rows reflect the
-sequence variation within a particular group. Their calculation is enabled
-by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
-the {\sl Annotation $\Rightarrow$ Autocalculated Annotation } submenu of the
-alignment window.
+% \subsubsection{Alignment and Group Sequence Logos}
+% \label{seqlogos}
-\subsubsection{Alignment and Group Sequence Logos}
-\label{seqlogos}
+% The consensus annotation row that is shown below the alignment can be overlaid
+% with a sequence logo that reflects the symbol distribution at each column of
+% the alignment. Right click on the Consensus annotation row and select the {\sl
+% Show Logo} option to display the Consensus profile for the group or alignment.
+% Sequence logos can be enabled by default for all new alignments {\sl via} the
+% Visual tab in the Jalview desktop's preferences dialog box.
+
+\section{Pairwise Alignments}
+Jalview can calculate optimal pairwise alignments between arbitrary
+sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option.
+Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
-The consensus annotation row that is shown below the alignment can be overlaid
-with a sequence logo that reflects the symbol distribution at each column of
-the alignment. Right click on the Consensus annotation row and select the {\sl Show
-Logo} option to display the Consensus profile for the group or alignment.
-Sequence logos can be enabled by default for all new alignments {\sl via} the
-Visual tab in the Jalview desktop's preferences dialog box.
+
+
+\exercise{Remove Redundant Sequences}{
+
+\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.}
+
+\exstep{In the {\sl Edit} menu select {\sl Remove Redundancy} to open the
+Redundancy threshold selection dialog. Adjust the redundancy threshold value, start
+at 50 and increase the value to 65. Sequences selected will change colour in the Sequence ID panel. Select ``Remove'' to
+remove the sequences that are more than 65\% similar under this alignment.}
+
+\exstep{From the tree window, select {\sl View $\Rightarrow$
+Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.} \exstep{Use the [Undo] button in the Redundancy threshold selection dialog box
+to recover the sequences. Note that the * symbols disappear from the tree display.}
+\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
+}
\exercise{Group Conservation Analysis}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
-\exstep{In the View menu, create a new view. Ensure the annotation panel
-is displayed (Show annotation in Annotations menu). Enable the display
-of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
-Autocalculated Annotation } submenu in the sequence alignment window. Then display of sequence
-logos to make it easier to see the different residue populations within each
-group. Activate logo by right clicking on the Consensus annotation row to open
-the pop-up menu and select the {\sl Show Logo} option.}
+tree based conservation analysis exercise (exercise \ref{consanalyexerc}).}
+\exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to
+create a new view. Ensure the annotation panel is displayed ({\sl Show annotation} in {\sl Annotations} menu). Enable the
+display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
+Autocalculated Annotation } submenu in the alignment window.}
+\exstep{Displaying the sequence
+logos will make it easier to see the different residue populations within each
+group. Activate the logo by right clicking on the Consensus annotation row to
+open the context menu and select the {\sl Show Logo} option.}
\exstep{In the column alignment ruler, select a column exhibiting about 50\%
-conservation that lies within the central conserved region of the alignment. Subdivide the alignment according to
-this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
+conservation that lies within the central conserved region of the alignment.
+(Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).}
+\exstep{Subdivide the alignment
+according to this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
\exstep{Re-order the alignment according to the new groups that have been
-defined. Click on the group annotation row IDs to select groups exhibiting a
+defined by selecting {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
+By Group}.
+
+Click on the group annotation row IDs to select groups exhibiting a
specific mutation.}
\exstep{Select another column exhibiting about 50\% conservation
overall, and subdivide the alignment further. Note that the new groups
inherit the names of the original groups, allowing you to identify the
-combination of mutations that resulted in the subdivision.
-}
+combination of mutations that resulted in the subdivision.}
\exstep{Clear the groups, and try to subdivide the alignment using two
non-adjacent columns.
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 See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
}
-\subsection{Other Calculations}
-
-
-\subsubsection{Pairwise Alignments}
-
-Jalview can calculate optimal pairwise alignments between arbitrary sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option. Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
-
\begin{figure}[]
\begin{center}
\includegraphics[width=4in]{images/pairwise.pdf}
\end{center}
\end{figure}
-\pagebreak[2]
\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
+% \ref{featuresfromdb} discusses the retrieval of database references and
+% establishment of sequence coordinate systems for the retrieval and display of
+% features from databases and DAS annotation services.
+% 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.
-This chapter describes the annotation, analysis, and visualization tasks that
-the Jalview Desktop can perform.
-
-Section \ref{wkwithstructure} introduces the structure visualization
-capabilities of Jalview. In Section \ref{alignanalysis}, you will find
-descriptions and exercises on building and displaying trees, PCA analysis,
-alignment redundancy removal, pairwise alignments and alignment conservation
-analysis. Section \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Section \ref{jabaservices} explains how to
-configure the Jalview Desktop for access to new JABAWS servers.
-Section \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS AACon
-service for protein multiple alignment conservation analysis.
-Section \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS protein disorder prediction
-services are introduced in Section \ref{protdisorderpred}.
-
-Section \ref{featannot} describes the mechanisms provided by Jalview for
-interactive creation of sequence and alignment annotation, and how they can be
-displayed, imported and exported and used to reorder the alignment. Section
-\ref{featuresfromdb} discusses the retrieval of database references and
-establishment of sequence coordinate systems for the retrieval and display of
-features from databases and DAS annotation services. Section
-\ref{workingwithnuc} describes functions and visualization techniques relevant
-to working with nucleotide sequences, coding region annotation and nucleotide
-sequence alignments.
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
\subsection{Viewing Structures}
\label{viewAllStructures}
-The structure viewer can be launched in two ways from the sequence ID context
+The structure viewer is launched 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
+alignment, select the sequence and right click the mouse to open context
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} opens a Structure Chooser dialog box.
+The second way is most useful if you want to view all structural data available for
+a set of sequences in an alignment. Select all the sequence ids in the sequence
+ID panel and right click the mouse to open context
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$}. If any of
+the {\bf currently selected} sequences have structures associated they will
+appear in the Structure Chooser dialog box. The structures can be ranked by
+different parameters, 'Best Quality' is defaul option. Select the
+structures required and click {\sl View} to open a structure viewer containing
the associated structures superposed according to the alignment.
-In both cases, each structure to be displayed will be downloaded or loaded from
+The structure to be displayed will be downloaded or loaded from
the local file system, and shown as a ribbon diagram coloured according to the
associated sequence in the current alignment view (Figure \ref{structure}
(right)). The structure can be rotated by clicking and dragging in the structure
automatic application of colour schemes when new structure data is added, or
when associated alignment views are modified.
-
-\exercise{Viewing Structures}{\label{viewingstructex}
+\exercise{Viewing Structures in Jmol viewer}{\label{viewingstructex}
\exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the
-sequence ID label of {\sl FER1\_SPIOL}, this brings up
-the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
-Associate Structure with Sequence $\Rightarrow$ Discover
-PDB IDs}. Jalview will now attempt to find PDB structures for the sequences in
-the alignment.
+\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}.
% JBP Note: Bug JAL-1238 needs to be fixed ASAP
-
-{\bf Note:} If you are using Jalview v2.8 - use the {\sl Uniprot } source from the {\sl Web services $\Rightarrow$ Fetch DB References $\Rightarrow$ ..} submenu of the Alignment Window to retrieve the PDB IDs. }
-\exstep{ Right-click on the sequence ID for {\sl FER1\_SPIOL}.
-Select { \sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$ View Structure
-$\Rightarrow$ 1A70}. A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel. } \exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
-\exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press OK to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with a suitable program. }
-\exstep{Select {\sl File $\Rightarrow$ View Mapping} from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.}
-\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file. Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
-
-\exstep{Right click on the structure in the submenu and bring up the Jmol
-window.
-Explore the menu options. Try to change the style of molecular display - by first using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.} \exstep{Use the {\sl File $\Rightarrow$ Save As .. } function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
-
+}
+\exstep{By default the Jmol
+structure viewer opens in the Jalview desktop. Rotate the molecule by clicking
+and dragging in the structure viewing box.
+Zoom with the mouse scroll wheel. }
+\exstep{Roll the
+mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment.
+Note that if a residue in the sequence maps to one in the structure, a label
+will appear next to that residue in the structure viewer.}
+\exstep{Move the mouse over the structure. In the Jmol viewer, placing the mouse over a
+part of the structure will bring up a tool tip indicating the name and number of that residue.
+In the alignment window, the corresponding residue in the sequence is
+highlighted in black.}
+\exstep{Clicking the alpha carbon toggles the highlight and residue label on and
+off.
+Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
+\exstep{In the structure viewer menu, select {\sl Colours $\Rightarrow$ Background
+Colour\ldots} and choose a suitable colour.
+Press {\sl OK} to apply this.}
+\exstep{Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the
+image. On your computer, view this with a suitable program. }
+\exstep{Select
+{\sl File $\Rightarrow$ View Mapping} from the structure viewer menu.
+A new window opens showing the residue by residue alignment between the sequence and the structure.}
+\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file.
+Once the file is saved, open the location in your file browser (or explorer
+window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu).
+Verify that you can open and view the associated structure from the sequence ID
+context menu's {\sl 3D Structure } submenu in the new alignment window.}
+
+\exstep{In the Jmol window, right click on the structure window and explore the
+menu options. Try to change the style of molecular display - for example by
+using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.}
+\exstep{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 See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
}
+\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.
+
+\exstep{First, Chimera must be downloaded and installed on the computer.
+Chimera program is available on the UCSF web site \textsf{https://www.cgl.ucsf.edu/chimera/download.html}.}
+\exstep{In the desktop menu, select {\sl Tool $\Rightarrow$ Preferences}. In
+the ``{\sl
+Structure}'' tab set {\sl Default structure viewer} as {\sl
+Chimera}; then click {\sl OK}.}
+\exstep{Close the Jalview program, from the
+{\sl Desktop menu} select {\sl Jalview $\Rightarrow$ Quit Jalview}. Then reopen
+Jalview, Chimera should open as the default viewer.}
+{\sl Note: The Jmol structure viewer sits within the Jalview desktop. However
+the Chimera structure viewer sits outside the Jalview desktop and a Chimera
+view window sits inside the Jalview desktop.}
+
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.} }
+
\subsection{Superimposing Structures}
\label{superposestructs}
Many comparative biomolecular analysis investigations aim to determine if the
biochemical properties of a given molecule are significantly different to its
homologues. When structure data is available, comparing the shapes of molecules
by superimposing them enables substructure that may impart different behaviour
-to be quickly identified. The identification of optimal 3D superpositions
+to be quickly identified. The identification of optimal 3D superposition
involves aligning 3D data rather than sequence symbols, but the result can
still be represented as a sequence alignment, where columns indicate positions
in each molecule that should be superposed to recreate the optimal 3D alignment.
Jalview can employ Jmol's 3D fitting routines\footnote{See
\href{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}
for more information.} to recreate 3D structure superpositions based on the
-correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view happens automatically if a
-structure is added to an existing Jmol display using the {\sl Structure
-$\Rightarrow$ View PDB Structure $\Rightarrow$ ..}. A new Jmol view containing
-superposed structures can also be created using the {\sl Structure
-$\Rightarrow$ View all {\bf N} PDB Structures} option (when {\bf {\sl N}}
-$>$ 1) if the current selection contains two or more sequences with associated
+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
+{\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} to open the Structure Chooser dialog box.
+Select 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 outputed to the Jalview
+Full information about the superposition is also outputted to the Jalview
console.\footnote{The Jalview Java Console is opened from {\sl Tools
$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
includes the precise atom pairs used to superpose structures.
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}
\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 {\bf 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. (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 ?} }
-
\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
\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
\exstep{Download the PDB file at
\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
-
This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
server.}
-
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
free memory available.
{\sl Use the following webstart link:
-
\href{http://www.jalview.org/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
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
+Service $\Rightarrow$ 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}).
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
+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.
to be unstructured or flexible, or alternately, fold to form globular domains.
As a consequence, disorder predictor results include both sequence features and
sequence associated alignment annotation rows. Section \ref{featannot} describes
-the manipulation and display of these data in detail, and {\bf Figure
-\ref{alignmentdisorder}} demonstrates how sequence feature shading and
+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}
-\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear. Note that the number of sequences in the results window is many more than in the original alignment as JNet performs a PSI-BLAST search to expand the prediction dataset.
-}
+\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 Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction}
+from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear.
+Note that the number of sequences in the results window is many more than in the original alignment as
+JNet performs a PSI-BLAST search to expand the prediction dataset. The results
+from the prediction are visible in the annotation panel. Jnet 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.
}
\exstep{
-Select the second sequence prediction, and copy and paste it into the first
-prediction window. You can now compare the two predictions. Jnet secondary structure prediction annotations are examples of {\bf sequence-associated alignment annotation}.
+Select the sequence used in the second sequence prediction by clicking on its
+name in the sequence ID panel, and copy {\sl ([CTRL] or [CMD]-C)} and then
+paste it {\sl [CTRL] or [CMD]-V)} into the first prediction window. You
+can now compare the two predictions as the annotations associated with the
+sequence has also been copied across.
% which is described in Section \ref{seqassocannot} below.
}
\exstep{
-Select and hide some columns in one of the profiles that were returned from the JNet service, and then submit the profile for prediction again.
+Select and hide some columns in one of the alignment profiles that were returned
+from the JNet service, and then submit the profile for prediction again.
}
\exstep{
When you get the result, verify that the prediction has not been made for the
-hidden parts of the profile, and that the JPred reliability scores differ from the prediction made on the full profile.
-
-{\sl Note: you may want to keep this data for use in exercise \ref{viewannotfileex}.}
+hidden parts of the profile (by clicking the mouse on column ruler and right click to open the
+context menu and select {\sl Reveal All}), and that the JPred reliability scores
+differ from the prediction made on the full profile.
}
\exstep{
-In the original alignment that you loaded in step 1, {\bf select all} sequences,
-then open the {\bf Sequence ID $\Rightarrow$ Selection } submenu and select the
-{\bf Add Reference Annotation} option.
+In the original alignment that you loaded in step 1, select {\bf all}
+sequences, then open the {\sl Sequence ID $\Rightarrow$ Selection } submenu
+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
+original alignment window.}
-The JNet predictions for the sequences should now be visible in the original
-alignment.} }
+{\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}. }
\begin{figure}[htbp]
\begin{center}
\subsubsection{Navigating Large Sets of Disorder Predictions}
-{\bf Figure \ref{alignmentdisorderannot}} shows a single sequence annotated with
+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
values are structured.
{\bf Disordered region} sequence features are created marking mark range(s) of residues with positive first order derivatives, and
-\textbf{Globular Domain} features mark long stretches of order. \textbf{Dydx} annotation rows gives the first order derivative of smoothed score. Values above 0 indicates
+\textbf{Globular Domain} features mark long stretches of order. \textbf{Dydx} annotation rows give the first order derivative of smoothed score. Values above 0 indicates
residue is disordered.
\textbf{Smoothed Score and Raw Score} annotation rows give the smoothed and raw scores used to create the differential signal that
\exercise{Protein Disorder Prediction}{
%\label{protdispredex}
-\exstep{Open the alignment at
+\exstep{Open the alignment at:
\url{http://www.jalview.org/tutorial/interleukin7.fa}. } also available at
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.}}
+the structures for all sequences. ({\sl Hint: see \ref{viewAllStructures} to see
+how to do this.})}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
-\exstep{Apply the IUPred disorder prediction method}
+\exstep{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 ?}}
\chapter{DNA and RNA Sequences}
\subsubsection{Retrieval of Protein or DNA Cross References}
The {\sl Calculate $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the protein product(s).
-\subsubsection{Retrieval of Protein DAS Features on Coding Regions}
+\subsubsection{Retrieval of Protein Features on Coding Regions}
-The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments. This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig. Jalview will use the Uniprot accession numbers associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using the coding region location.
+The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments.
+This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig.
+Jalview will use the Uniprot accession numbers associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using
+the coding region location.
\begin{figure}[htbp]
\begin{center}
\label{dnadasfeatures}
\includegraphics[width=5in]{images/dnadasfeatures.pdf}
-\caption{Uniprot and PDB sum features retrieved {\sl via} DAS and mapped onto
+\caption{Uniprot and PDB sum features retrieved and mapped onto
coding regions of EMBL record V00488 (an earlier version of Jalview is shown
here).}
{
\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the
-alignment view format to Wrapped mode so the distinct exons can be seen.}
+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}
window {\sl View $\Rightarrow$ Features setting}
and fetch features for D49489 from the Uniprot reference server,
\exercise{Viewing RNA Structures}
{ \label{viewingrnaex}
-\exstep{Import RF00162 from Rfam (Full) using Fetch sequence(s) option in File
-menu.}
+\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.}
Base Pair probabilities. Explore how editing the alignment affects the consensus
calculation.}
-\exstep{Import 2GIS from PDB database using Fetch sequence(s) option.}
+\exstep{Import 2GIS from PDB database using {\sl Fetch sequence(s)} option.}
\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.}
which were introduced in in Section \ref{fetchseq}, provide sequence and
alignment data. They can also be used to add sequence IDs to an alignment
imported from a local file, prior to further annotation retrieval, as described
-in Section \ref{featuresfromdb}. A second type of one way service is provided
-by Jalview's DAS sequence feature retrieval system, which is described
-in Section \ref{dasfretrieval}.
+in Section \ref{featuresfromdb}.
% The final type of one way service are sequence
% and ID submission services.
% exemplified by the `Envision2 Services' provided
git://source.jalview.org / jalview-manual.git / blobdiff