\newtheorem{definition}{Definition}
-\title{Jalview 2.5: A manual and introductory tutorial }
+\title{Jalview 2.10.3: A manual and introductory tutorial }
\author{David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,Suzanne Duce and Geoff Barton}
\date{Manual version 1.2.3 6th May 2011}
{\Huge
-Jalview 2.10.1}
+Jalview 2.11}
\vspace{0.5in}
{\huge
{\large
-David Martin, James Procter
+David Martin, James Procter, Ben Soares
Andrew Waterhouse, Saif Shehata, Nancy Giang
Dundee, Scotland DD1 5EH, UK
\vspace{2in}
-Manual Version 1.9.1
+Manual Version 1.9.3
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-17th November 2017
+10th May 2019
\end{center}
\clearemptydoublepage
-% ($Revision$) 11th October 2010.}
+% ($Revision: 1.55 $) 11th October 2010.}
% TODO revise for 2.6
\pagenumbering{roman}
There are two types of Jalview program. The {\bf Jalview Desktop} is a standalone
application that provides powerful editing, visualization, annotation and
-analysis capabilities. The {\bf JalviewLite} applet has the same core
+analysis capabilities. The {\bf JalviewJS} that has the same core
visualization, editing and analysis capabilities as the desktop, without the
-desktop's webservice and figure generation capabilities. It is designed to be
-embedded in a web page,\footnote{A demonstration version of Jalview (Jalview Micro
-Edition) also runs on a mobile phone but the functionality is limited to sequence
-colouring.} and includes a javascript API to allow customisable display of
-alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
+desktop's webservice. It is designed to be
+opened in a web browser,\footnote{A demonstration version of Jalview (Jalview Micro
+Edition) also runs on a mobile phone but the functionality is limited.} and includes a javascript API.
The Jalview Desktop provides access to protein and nucleic acid sequence, alignment and structure
\subsection{About this Tutorial }
This tutorial is written in a manual format with short exercises where
-appropriate, typically at the end of each section. The first few sections concerns the
+appropriate. The first few sections concerns the
basic operation of Jalview and should be sufficient for those who want to
launch Jalview (Section \ref{startingjv}), open an alignment (Section
\ref{loadingseqs}), perform basic editing (Section
analysis techniques available in Jalview. These include working
with the embedded Jmol molecular structure viewer (or UCSF Chimera), building
and viewing trees and Principal Components Analysis (PCA) plots, and using
-trees for sequence conservation analysis. An overview of
-the Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
-the alignment and secondary structure prediction services are described
+trees for sequence conservation analysis. Section \ref{featannot} details the creation and visualization of sequence,
+features and alignment annotation. The alignment and secondary structure prediction services are described
in detail in Sections \ref{msaservices} and \ref{protsspredservices}
-respectively.
-Section \ref{featannot} details the creation and visualization of sequence,
-features and alignment annotation. Section \ref{workingwithnuc} discusses
-specific features of use when working with nucleic acid sequences, such as translation and linking to protein coding regions, and the display and analysis of RNA secondary structure.
+respectively. 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. An overview of
+the Jalview Desktop's webservices is given in Section \ref{jvwebservices}.
%^Chapter \ref{jalviewadvanced} The third chapter covers the detail^ of Jalview and is aimed at the user who is
%already familiar with Jalview operation but wants to get more out of their
e.g.} [CTRL]-C means press [CTRL] and the `C' key simultaneously).
Menu options are given as a path from the menu
-that contains them - for example {\sl File $\Rightarrow$ Input Alignment
+that contains them. For example {\sl File $\Rightarrow$ Input Alignment
$\Rightarrow$ From URL} means to select the `From URL' option from the `Input
Alignment' submenu of a window's `File' dropdown menu.
This tutorial is based on the Jalview
Desktop application. Much of the information will also be useful for users of
-the JalviewLite applet, which has the same core editing, analysis and visualization capabilities. The Jalview Desktop, however, is much more powerful, and
+the JalviewJS, which has the same core editing, analysis and visualization capabilities. The Jalview Desktop, however, is much more powerful, and
includes additional support for interaction with external web services, and
production of publication quality graphics.
The Jalview Desktop can be run in two ways; as an application launched from the
web {\sl via} Java webstart, or as an application loaded onto your hard drive.
-The webstart version is launched from the pink `Launch Jalview Desktop
+The webstart version is launched from the `Launch Jalview Desktop
button' at the top right hand side of pages of the website
\href{http://www.jalview.org}{(www.jalview.org)}.
To download the locally installable version, follow the links on the download
%% this paragraph needs to be rewritten for the new signed certificate from Certum.
-When the application is launched with webstart, two dialogs may appear before
+When the application is launched with webstart, 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 program to handle the webstart
\exstep {If
you are having trouble, it may help changing the browser you are using, as the browsers and
its version may affect this process.}
-\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
+\exstep{To disable opening of the demonstration project during the launch, go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. A `Preference'
dialog box opens, untick the box adjacent to the `Open file' entry in the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
the URL history button (a downward arrow on the right hand side of the dialog
box) to view the files, select exampleFile\_2\_7.jar
-(\url{http://www.jalview.org/examples/exampleFile_2_3.jar})
+(\url{http://www.jalview.org/examples/exampleFile_2_7.jar})
then click {\sl OK}.}
-{\bf Note:} Should you want to load your own sequence during the launch process, then go
+\begin{list}{$\circ$}{\newline
+ \newline {\bf
+ Notes}}
+
+\item {To make Jalview display a different alignment when it is launched, 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.
-
-
-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 the jnlp file will allow Jalview to be launched offline.
+Preferences...} menu on the desktop. Then tick the `Open file' entry of `Visual'
+preferences tab, type in the URL of the sequence you want to load.}
+\item {You may want to move the jalview.jnlp file from your {\bf downloads} to another folder.}
+\item {Opening Jalview via the jnlp file will also allow Jalview to be launched offline.}
+\end{list}
{\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.}
\subsubsection{Email Lists}
-The Jalview Discussion list {\tt jalview-discuss@jalview.org} provides a forum
+The Jalview Discussion list ({\tt jalview-discuss@jalview.org}) provides a forum
for Jalview users and developers to raise problems and exchange ideas - any
problems, bugs, and requests for help should be raised here. The {\tt
jalview-announce@jalview.org} list can also be subscribed to if you wish to be
Jalview has two navigation and editing modes: {\bf normal mode}, where
editing and navigation is performed using the mouse, and {\bf cursor mode}
- where editing and navigation are performed using the keyboard. The {\bf F2 key}
- is used to switch between these two modes.
+ where editing and navigation are performed using the keyboard. The {\bf F2}
+ key is used to switch between these two modes.
{\em Note:} On MacBooks and other laptops with compact keyboards, you may need
- to press the {\bf function key [Fn]} when pressing any of the numbered function
- keys. So to toggle between keyboard and normal mode, press [Fn]-[F2].
+ to press the function key {\bf [Fn]} when pressing any of the numbered function
+ keys. So to toggle between keyboard and normal mode, press {\bf [Fn]-[F2]}.
\begin{figure}[htb]
\begin{center}
\includegraphics[width=6.5in]{images/jalview_anatomy.pdf}
-\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labeled.}
+\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop
+Application are labeled.}
% TODO: modify text labels to be clearer - black on grey and black border for clarity
\label{anatomy}
\end{center}
Each alignment view shown in the alignment window presents a window onto the
visible regions of the alignment. This means that with anything more than a few
residues or sequences, alignments can become difficult to visualize on the
- screen because only a small area can be shown at a time. It can help,
- especially when examining a large alignment, to have an overview of the whole
- alignment. Select {\sl View $\Rightarrow$ Overview Window} from the Alignment
- window menu bar (Figure \ref{overview}\footnote{the menu shown in this figure
- is from Jalview 2.2, later versions have more options.}).
+ screen because only a small area can be shown at a time. Here, it helps, to
+ have an overview of the whole alignment, especially when it is large.
+ Select {\sl View $\Rightarrow$ Overview Window} from the Alignment
+ window menu bar (Figure \ref{overview}).
% (Figure4)
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/overview.pdf}
-\caption{{\bf Alignment Overview Window.} The overview window for a view is opened from the {\em View} menu.}
+\caption{{\bf Alignment Overview Window.} The overview window for a view is
+opened from the {\em View} menu.}
\label{overview}
\end{center}
\end{figure}
The red box in the overview window shows the current view in the alignment
window. A percent identity histogram is plotted below the alignment overview.
-Shaded parts indicate rows and columns of the alignment that are hidden (in this
-case, a single row at the bottom of the alignment - see Section
+Shaded parts indicate rows and columns of the alignment that are hidden (for more information see Section
\ref{hidingregions}). You can navigate around the alignment by dragging the red
box.
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, the key
-combination {\bf Fn key and F2} is needed, as button is
+The {\bf F2} key is used to switch between these two modes. With a Mac, the key
+combination {\bf Fn and F2} keys are needed, as the {\bf F2} 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
+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}
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
+\exstep{Find the Overview Window, {\sl View
$\Rightarrow$ 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
column 13 by typing {\bf 1 3 , 5} [RETURN].}
{\bf Note:} To view Jalview's comprehensive on-line help documentations select
-{\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.
+{\sl Help} in desktop window menu, clicking on {\sl Documentation} will open a
+Documentation window. Select topics from the navigation panel on the left hand
+side or use the Search tab to locate specific key words.
{\sl\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.}
% tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
\subsection{Drag and Drop}
In most operating systems you can drag a file icon from a file browser
- window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended.
+ window and drop it on an open Jalview application window. The file will then be opened as a new alignment window.
+ %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended.
Drag and drop also works when loading data from a URL -
simply drag the link or url from the address panel of your browser onto an
alignment or the Jalview desktop background and Jalview will load data from the
\subsection{From a File}
Jalview can read sequence alignments from a sequence alignment file. This is 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
+wordprocessor document see Cut and Paste (Section \ref{cutpaste}). Select
{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main
menu (Figure \ref{loadfile}). You will then get a file selection window where
you can choose the file to open. Remember to select the appropriate file type.
manually locate and save sequences from a web page before loading them into
Jalview. It also allows Jalview to gather additional metadata provided by the
source, such as annotation and database cross-references.
-Select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and
-a window will appear (Figure \ref{loadseq}). Pressing the database selection
-button in the dialog box opens a new window showing all the database sources
-Jalview can access (grouped by the type of database). Once you've selected the
-appropriate database, hit OK close the database selection window, and then enter
-one or several database IDs or accession numbers separated by a semicolon and
-press OK. Jalview will then attempt to retrieve them from the chosen database.
-Example queries are provided for some databases to test that a source is
-operational, and can also be used as a guide for the type of accession numbers
-understood by the source.
+
+To begin retrieving data, select {\sl File $\Rightarrow$ Fetch Sequences \ldots}
+from the main menu. A window will then appear (Figure \ref{loadseq}) showing all
+the database sources Jalview can access (grouped by the type of database). Once
+you've selected the appropriate database by double clicking it or hitting OK, the
+database selection window will close and the sequence fetcher for that database
+will appear. You can then enter one or several database IDs or accession numbers
+separated by a semicolon and press OK. Jalview will then attempt to retrieve them
+from the chosen database. Example queries are provided for some databases to test
+that a source is operational, and can also be used as a guide for the type of
+accession numbers understood by the source.
% [fig 9]
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsection{Memory Limits}
-\label{memorylimits}
-Jalview is a Java program. One unfortunate implication of this is that Jalview
-cannot dynamically request additional memory from the operating system. It is
-important, therefore, that you ensure that you have allocated enough memory to
-work with your data. On most occasions, Jalview will warn you when you have
-tried to load an alignment that is too big to fit in to memory (for instance,
-some of the PFAM alignments are {\bf very} large). You can find out how much
-memory is available to Jalview with the desktop window's {\sl $\Rightarrow$
-Tools $\Rightarrow$ Show Memory Usage} function, which enables the display of
-the currently available memory at the bottom left hand side of the Desktop
-window's background. Should you need to increase the amount of memory available
-to Jalview, full instructions are given in the built in documentation (opened by
-selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory
-parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
\exercise{Loading Sequences}{
\label{load}
\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
close all windows.}
-\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
+%% TODO: omit or combine this exercise
+%% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
+\exstep{{\bf Loading sequences from URL:} Selecting {\sl File $\Rightarrow$
Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
Click {\sl OK} to load the alignment.}
+%%TODO: omit or combine
\exstep{{\bf Loading sequences from a file:} Close all windows using the
{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and save the file to your desktop using {\sl File
+your web browser and save the fasta file (.fa) file to your desktop using {\sl File
$\Rightarrow$ Save Page as}.
Open the file you have just saved in Jalview by selecting {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
Select the file and click {\sl OK} to load.}
\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+
(i) Drag the alignment.fa file that you have just saved from its folder and
drop it onto the Jalview desktop window, the alignment should open.
split window opens in the Jalview desktop.
}
-\exstep{{\bf The text editor:} (i) Open the alignment.fa file using text editor.
+\exstep{{\bf The text editor:}
+
+(i) Open the alignment.fa file using text editor.
Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
-(ii) Place the mouse on the Jalview desktop and right-click the mouse
+(ii) Move the mouse pointer onto the Jalview desktop window's background and right-click
to open the context window. Select the {\sl Paste to New Window} menu option.
(iii) In the Jalview desktop menu, select {\sl File
and the alignment will be loaded.}
\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
-$\Rightarrow$ Fetch Sequence(s)...} from the Jalview desktop menu. The {\sl
+$\Rightarrow$ Fetch Sequences...} from the Jalview desktop menu. The {\sl
Select Database Retrieval Source} dialog will open listing all the database
sources. Select the {\bf PFAM seed} database and click {\sl OK}.
+%TODO fix ss appearing as RNA ss issue with secondary structure from pfam when downloading the Full alignment.
+
(ii) The {\sl New
Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
and click {\sl OK}.
{\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}} }
+\subsection{Memory Limits}
+\label{memorylimits}
+Jalview 2.11 and later will automatically maximise the amount of memory available,
+but if you are using an earlier version or launching Jalview in a specialised way
+you may need ensure that you have allocated enough memory to
+work with your data. On most occasions, Jalview will warn you when you have
+tried to load an alignment that is too big to fit in to memory (for instance,
+some of the PFAM alignments are {\bf very} large). You can find out how much
+memory is available to Jalview with the desktop window's {\sl $\Rightarrow$
+Tools $\Rightarrow$ Show Memory Usage} function, which enables the display of
+the currently available memory at the bottom left hand side of the Desktop
+window's background. Should you need to increase the amount of memory available
+to Jalview, full instructions are given in the built in documentation (opened by
+selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory
+parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
+
\section{Saving Sequences and Alignments}
\label{savingalignments}
\subsection{Saving Alignments} Jalview allows alignments to be saved to file
%[fig 10]
\begin{figure}[htbp]
\begin{center}
-\parbox[c]{1.0in}{
-\includegraphics[width=1.0in]{images/saveas.pdf}
+\parbox[c]{3.0in}{
+\includegraphics[width=3in]{images/saveas.pdf}
}
-\parbox[c]{4in}{
-\includegraphics[width=4in]{images/saveas2.pdf}
+\parbox[c]{3in}{
+\includegraphics[width=3in]{images/saveas2.pdf}
}
\caption{{\bf Saving alignments in Jalview to disk.}}
\label{savealign}
dialog box will appear. Loading a project will restore Jalview to exactly the
view at which the file was saved, complete with all alignments, trees,
annotation and displayed structures rendered appropriately.
-} \parbox[c]{2in}{ \centerline {
-\includegraphics[width=1.5in]{images/saveproj.pdf} }}
+} \parbox[c]{2.3in}{ \centerline {
+\includegraphics[width=2.2in]{images/saveproj.pdf} }}
\exercise{Saving Alignments}{
\label{save}
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}.}
+Enter a file name, select file type 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 steps saving the files in different file formats.}
}
\exstep{Ensure at least one alignment window is active in Jalview. Open the
overview window {\sl View $\Rightarrow$ Overview Window}
- and scroll red box to any part of the alignment.
+ and click and drag to move the red box to any part of the alignment.
Select {\sl File
-$\Rightarrow$ Save Project} from the main menu and save the project in a
+$\Rightarrow$ Save Project} from the desktop window menu and save the project in a
suitable folder.}
\exstep{Close all windows and then load the project {\sl via} the {\sl File
$\Rightarrow$ Load Project} menu option. Observe how many of the windows
-reopen. Are they the same as were saved. } {\bf See the video at:
+reopen. Are they the same as when they were saved ? } {\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.} }
\end{center}
\end{figure}
+To select multiple complete sequences, click and drag the mouse down the
+sequence ID panel. The same techniques can be used as for columns above ([SHIFT]-Click for continuous and [CTRL]-Click (or {\sl
+[CMD]-Click} for Mac) to select discontinuous
+ranges of sequences (Figure \ref{selectrows}).
+%[fig 14]
+
\subsection{Selecting Sequences}
\begin{figure}[htb]
\begin{center}
\includegraphics[width=4in]{images/select3.pdf}
-\caption{{\bf Selecting multiple sequences in an alignment.} Use [CTRL] or [SHIFT] to select many sequences at once.}
+\caption{{\bf Selecting multiple sequences in an alignment.} Use [CTRL] or
+[SHIFT] to select many sequences at once.}
\label{selectrows}
\end{center}
\end{figure}
-To select multiple complete sequences, click and drag the mouse down the
-sequence ID panel. The same techniques as used for columns (above) can be used
-with [SHIFT]-Click for continuous and [CTRL]-Click (or
-[CMD]-Click for Mac) to select discontinuous
-ranges of sequences (Figure \ref{selectrows}).
-%[fig 14]
+
\subsection{Making Selections in Cursor Mode}
$\Rightarrow$ Invert Sequence/Column Selection} in the alignment window.
Inverting the selection is useful when selecting large regions in an alignment,
simply select the region that is to be kept unselected, and then invert the selection.
-This may also be useful when hiding large regions in an alignment (see Section \ref{hidingregions}
-below).
+This may also be useful when hiding large regions in an alignment (see Section \ref{hidingregions}).
Instead of selecting the columns and rows that are to be hidden, simply select the
region that is to be kept
visible, invert the selection, then select {\sl View $\Rightarrow$ Hide
created which are labeled regions of the alignment. To create a group, first
select the region which is to comprise the group. Then click the right mouse
button on the selection to bring up a context menu. Select {\sl Selection
-$\Rightarrow$ Group $\Rightarrow$ Edit name and description of
+$\Rightarrow$ Edit New 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 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.
+By default the new group will have a box drawn around it. The appearance of the group can be changed (see Section \ref{colours}).
+This group will stay defined even when the selection is removed.
+
+
+\section{Exporting the Current Selection}
+The current selection can be copied to the clipboard (in PFAM format). It can
+also be output to a textbox using the output functions in the pop-up menu
+obtained by right clicking the current selection. The textbox enables quick
+manual editing of the alignment prior to importing it into a new window (using
+the {\sl New Window} button) or saving to a file with the {\sl File
+$\Rightarrow$ Save as } pulldown menu option from the text box.
\exercise{Making Selections and Groups}{
\label{exselect}
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' IDs - both selected and
+Hold down [CTRL] (or [CMD] on Mac) 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 columns by clicking on the Alignment Ruler. Note
\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 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{The current selection can be exported and saved, place mouse on the text
+area and right clicking the mouse to open the Sequence ID context menu.
+Select appropriate menu option and pick an output format (eg BLC) from the
+{\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
}
\exstep{In the Alignment output window that opens, try manually editing the
alignment before clicking the {\sl New Window} button. This opens the
% more? change colouring style. set border colour.
}
-\section{Exporting the Current Selection}
-The current selection can be copied to the clipboard (in PFAM format). It can
-also be output to a textbox using the output functions in the pop-up menu
-obtained by right clicking the current selection. The textbox enables quick
-manual editing of the alignment prior to importing it into a new window (using
-the {\sl New Window} button) or saving to a file with the {\sl File
-$\Rightarrow$ Save As } pulldown menu option from the text box.
\section{Reordering an Alignment}
-Sequence reordering is simple. Highlight the sequences to be moved then press the up or down arrow keys as appropriate (Figure \ref{reorder}). If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and then move the group rather than the individual sequence.
+Sequence reordering is simple. Highlight the sequences to be moved then press the up or down arrow keys ($\uparrow$, $\downarrow$) as appropriate (Figure \ref{reorder}).
+If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and
+then move the group rather than the individual sequence.
\begin{figure}[htbp]
\begin{center}
\section{Hiding Regions}
\label{hidingregions}
-It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create the several different views in the example alignment file that is loaded when Jalview is first started (See Figure \ref{startpage}).
+It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them.
+Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create
+the several different views in the example alignment file that is loaded when Jalview is first started (see Figure \ref{startpage}).
To hide a set of sequences, select them and right-click the mouse on the
selected sequence IDs to bring up the context pop-up menu. Select {\sl Hide
-Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
+Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}).
+To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
\begin{figure}[htbp]
\begin{center}
-\includegraphics[width=1.5in]{images/hide1.pdf}
-\includegraphics[width=2.5in]{images/hide2.pdf}
-\includegraphics[width=1.75in]{images/hide3.pdf}
-\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small blue
-triangle in the sequence ID panel.}
+\includegraphics[width=1.9in]{images/hide1.pdf}
+\includegraphics[width=2.7in]{images/hide2.pdf}
+\includegraphics[width=1.8in]{images/hide3.pdf}
+\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small
+blue triangle in the sequence ID panel.}
\label{hideseq}
\end{center}
\end{figure}
\begin{figure}[htbp]
\begin{center}
-\includegraphics[width=2in]{images/hide4.pdf}
+\includegraphics[width=1.7in]{images/hide4.pdf}
\includegraphics[width=3in]{images/hide5.pdf}
-\includegraphics[width=1in]{images/hide6.pdf}
+\includegraphics[width=1.2in]{images/hide6.pdf}
\caption{{\bf Hiding Columns} Hidden columns are represented by a small blue
triangle in the ruler bar.}
\label{hidecol}
It is often easier to select the region that you intend to work with, rather
than the regions that you want to hide. In this case, select the required region and use the {\sl View $\Rightarrow$ Hide
-$\Rightarrow$ All but Selected Region } menu entry, or press [Shift]+[Ctrl]+H
+$\Rightarrow$ All but Selected Region } menu entry, or press [SHIFT]-[CTRL]-H
to hide the unselected region.
\subsection{Representing a Group with a Single Sequence}
Note, any alignment edits that affect the sequence will also affect the whole
sequence group.
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit1.pdf}
+\includegraphics[width=3in]{images/edit2.pdf}
+\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
+selected sequence is dragged to the right while pressing and holding [SHIFT].}
+\label{gapseq}
+\end{center}
+\end{figure}
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit3.pdf}
+\includegraphics[width=3in]{images/edit4.pdf}
+\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
+group is dragged to the right with [CTRL] pressed.}
+\label{gapgroup}
+\end{center}
+\end{figure}
+
+%% TODO introduce select/hide by annotation here
+%% favor coverage of these core interactions (hide, show, select, reorder, multiple view)
+%% TODO - if columns are selected, then View->hide selected region hides *all* sequences, but it should leave the unselected columns visible !
+
\exercise{Hiding and Revealing Regions}{
\label{hidingex}
\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
}
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit1.pdf}
-\includegraphics[width=3in]{images/edit2.pdf}
-\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
-selected sequence is dragged to the right while pressing and holding [SHIFT].}
-\label{gapseq}
-\end{center}
-\end{figure}
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit3.pdf}
-\includegraphics[width=3in]{images/edit4.pdf}
-\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
-group is dragged to the right with [CTRL] pressed.}
-\label{gapgroup}
-\end{center}
-\end{figure}
\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).
+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], [CTRL] or [CMD] (Mac) 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
+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
\subsection{Introducing Gaps in a Single Sequence}
To introduce a gap, first select the sequence in the sequence ID panel and
then place the cursor on the residue to the immediate right of where the gap
-should appear. Hold down the SHIFT key and the left mouse button, then drag the sequence to the right until the required number of gaps has been inserted.
+should appear. Hold down the [SHIFT] key and the left mouse button, then drag the sequence to the right until the required number of gaps
+has been inserted.
-One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
+One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long.
+Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
\subsection{Introducing Gaps in all Sequences of a Group}
To insert gaps in all sequences in a selection or group, select the
required sequences in the sequence ID panel and then place the mouse cursor on
-any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
+any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the [CTRL] key
+and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
Gaps can be removed by dragging the residue to the immediate right of the gap
leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences).
-\newpage
+\subsection{Sliding Sequences}
+Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
+sequences are selected will ``slide'' the entire selected sequences to the left
+or right (respectively). Slides occur regardless of the region selection -
+which, for example, allows you to easily reposition misaligned subfamilies
+within a larger alignment.
+% % better idea to introduce hiding sequences, and use the invert selection, hide
+% others, to simplify manual alignment construction
+
+
+
+\subsection{Editing in Cursor Mode}
+Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
+pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
+under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
+press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
+or [SHIFT]-[SPACE] (both keys held down together).
+
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
+have everything unselected by pressing [ESC]. The gap under the cursor will be
+removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
+will be deleted up to the number specified. To delete gaps from all sequences of
+a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
+together). Note that the deletion will only occur if the gaps are in the same
+columns in all sequences in the selected group, and those columns are to the
+right of the selected residue.
+
\exercise{Editing Alignments}
%\label{mousealedit}
\label{editingalignex}
You are going to manually reconstruct part of the example Jalview
alignment available at
- \href{http://www.jalview.org/examples/exampleFile.jar}
- {http://www.jalview.org/examples/exampleFile.jar}.
+ \href{http://www.jalview.org/examples/exampleFile.jvp}
+ {http://www.jalview.org/examples/exampleFile.jvp}.
{\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
for key combinations such as [CTRL]-A. }
\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
+\exstep{ Select the first 7 sequences, and press H key to hide them (or right click
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 residue A lies at column 57 using the $\Rightarrow$
+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
{\sl Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
-deselect FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they
+deselect FER1\_MAIZE), and use the $\rightarrow$ key to slide them to so they
begin at column 5 of the alignment view.}}
\exstep{ Select all the visible
sequences (those not hidden) in the block by pressing [CTRL]-A.
Insert a single
gap in all selected sequences at column 38 of the alignment by holding [CTRL]
-and clicking on the R at column 38 in the FER1\_SPIOL, then drag one
+and clicking on the residue R at column 38 in the FER1\_SPIOL, then drag one
column to right.
Insert another gap at column 47 in all sequences in the same way.}
backwards and replay the edits you have made.}
}
-\subsection{Sliding Sequences}
-Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the entire selected sequences to the left
-or right (respectively). Slides occur regardless of the region selection -
-which, for example, allows you to easily reposition misaligned subfamilies
-within a larger alignment.
-% % better idea to introduce hiding sequences, and use the invert selection, hide
-% others, to simplify manual alignment construction
-
-\subsection{Editing in Cursor mode}
-Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
-pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
-under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
-press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
-or [SHIFT]-[SPACE] (both keys held down together).
-
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
-have everything unselected by pressing ESC. The gap under the cursor will be
-removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
-will be deleted up to the number specified. To delete gaps from all sequences of
-a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
-together). Note that the deletion will only occur if the gaps are in the same
-columns in all sequences in the selected group, and those columns are to the
-right of the selected residue.
-
\exercise{Keyboard Edits}
{
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using 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].}
+{\sl Reveal All}. Enter cursor mode by pressing [F2] (or [Fn]-[F2] (Mac)).}
% TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
\exstep{Insert 58 gaps at the start of the sequence 1 (FER\_CAPAA). Press
insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are
now aligned.}}
+
\chapter{Colouring Sequences and Figure Generation}
\label{colouringfigures}
\section{Colouring Sequences}
Colouring sequences is a key aspect of alignment presentation. Jalview allows
you to colour the whole alignment, or just specific groups. Alignment and
group colours are rendered
-{\sl below} any other colours, such as those arising from sequence features
+{\bf below} any other colours, such as those arising from sequence features
(these are described in Section \ref{featannot}). This means that if you
try to apply one of the colourschemes described in this section, and nothing
appears to happen, it may be that you have sequence feature annotation
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
-Show Features} option before you can see your colourscheme.
+Show Sequence Features} option before you can see your colourscheme.
There are two main types of colouring styles: {\bf simple static residue}
colourschemes and {\bf dynamic schemes} which use conservation and consensus
analysis to control colouring. {\bf Hybrid colouring} is also possible, where
-static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
+static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme}.
\subsection{Colouring the Whole Alignment}
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 {\bf
not} selected.
- This must be turned {\sl off} specifically as it is {\sl on} by default.
+ This must be turned {\bf off} specifically as it is {\bf 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.
\includegraphics[width=2in]{images/colourcons1.pdf}
\includegraphics[width=2in]{images/colourcons3.pdf}
\includegraphics[width=2in]{images/colourcons5.pdf}
-\caption{{\bf Conservation Shading} The density of the ClustalX style residue colouring is controlled by the conservation threshold. The effect of 0\% (left), 50\% (center) and 100\% (right) thresholds are shown.
+\caption{{\bf Conservation Shading} The density of the ClustalX style residue
+colouring is controlled by the conservation threshold. The effect of 0\% (left), 50\% (center) and 100\% (right) thresholds are shown.
}
\label{colcons}
\end{center}
\label{colscheme}
Full details on each colour scheme can be found in the Jalview on-line help. A brief description of each one is provided below:
-\subsubsection{ClustalX}
+\subsubsection{Clustalx}
\parbox[c]{3.5in}{This is an emulation of the default colourscheme used for alignments in ClustalX, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type. }
\parbox[c]{3in}{\includegraphics[width=2.75in]{images/col_clustalx.pdf}}
-\subsubsection{Blosum62}
+\subsubsection{Blosum62 Score}
\parbox[c]{3.5in}{Gaps are coloured white. If a residue matches the consensus sequence residue at that position it is coloured dark blue. If it does not match the consensus residue but the Blosum62 matrix gives a positive score, it is coloured light blue.}
\parbox[c]{3in}{
\subsubsection{Percentage Identity}
\parbox[c]{3.5in}{
-The Percent Identity option colours the residues (boxes and/or text) according to the percentage of the residues in each column that agree with the consensus sequence. Only the residues that agree with the consensus residue for each column are coloured.
+The Percentage Identity option colours the residues (boxes and/or text) according to the percentage of the residues in each column that agree with the consensus sequence. Only the residues that agree with the consensus residue for each column are coloured.
}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_percent.pdf}
\subsubsection{Zappo}
\parbox[c]{3.5in}{
-The residues are coloured according to their physicochemical properties. The physicochemical groupings are Aliphatic/hydrophobic, Aromatic, Positive, Negative, Hydrophillic, conformationally special, and Cyst(e)ine.
+The residues are coloured according to their physicochemical properties. The physicochemical groupings are Aliphatic/hydrophobic, Aromatic,
+Positive, Negative, Hydrophillic, Conformationally special, and Cyst(e)ine.
}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_zappo.pdf}
sequences and alignments.
} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_nuc.pdf} }
-\subsubsection{Purine Pyrimidine}
+\subsubsection{Purine/Pyrimidine}
\parbox[c]{3.5in}{ Residues are coloured according to whether the corresponding
nucleotide bases are purine (magenta) or pyrimidine (cyan) based. All non ACTG
residues are uncoloured. For further information about working with nucleic acid
} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_purpyr.pdf} }
-\subsubsection{RNA Helix Colouring}
+\subsubsection{By RNA Helices}
\parbox[c]{3.5in}{ Columns are coloured according to their assigned RNA helix as
defined by a secondary structure annotation line on the alignment. Colours for
each helix are randomly assigned, and option only available when an RNA
\begin{figure}[htbp]
\begin{center}
-\includegraphics[width=2.5in]{images/col_user1.pdf}
+\includegraphics[width=2.1in]{images/col_user1.pdf}
\includegraphics[width=2in]{images/col_user2.pdf}
-\includegraphics[width=1.75in]{images/col_user3.pdf}
-\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
+\includegraphics[width=2.1in]{images/col_user3.pdf}
+\caption{{\bf Creation of a user defined colour scheme.} Residue types are
+assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
\label{usercol}
\end{center}
\end{figure}
\exercise{Colouring Alignments}{
\label{color}
-Note: Before you begin this exercise, ensure that the {\sl Apply Colour
+Note: 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 $\Rightarrow$
-Clustal} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
+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
+\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62 score}. 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
+$\Rightarrow$ Blosum62 score} 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 selected group,
-not the whole alignment (this also explains the colouring changes observed in exercise
+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}.
\exercise{User Defined Colour Schemes}{
\label{colouex}
-\exstep{Load a sequence alignment. Ensure that the {\sl Colour $\Rightarrow$
+\exstep{Load a sequence alignment PF03460 from the PFAM
+seed database. Ensure that the {\sl Colour $\Rightarrow$
None} is selected. Select the alignment menu option {\sl Colour $\Rightarrow$
User Defined}.
A dialog window will open.}
{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}} }
+\exercise{Alignment Layout}{
+\label{exscreen}
+\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jvp}.
+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 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 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 on the annotations name and
+dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}.
+The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
+\exstep{Move the mouse to the top left hand corner of the annotation labels -
+a up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
+by clicking and dragging this icon up or down.}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+
\section{Formatting and Graphics Output}
\label{layoutandoutput}
Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output,
\subsection{Multiple Alignment Views}
-Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\sl Views}.
+Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\bf Views}.
Because each view displays the same underlying data, any edits performed in one view will update the alignment or annotation visible in all views.
\parbox[c]{4in}{Alignment views are created using the {\sl View $\Rightarrow$
New View} option of the alignment window or by pressing [CTRL]-T.
This will create a new view with the same groups, alignment layout and display options as the current one.
-Pressing G will gather together Views as named tabs on the alignment window, and pressing X will expand gathered Views so they can be viewed
-simultaneously in their own separate windows. To delete a group, press [CTRL]-W.}\parbox[c]{2.75in}{
+Pressing G key will gather together Views as named tabs on the alignment window, and pressing X key will expand gathered Views so they can be viewed
+simultaneously in their own separate windows.} \parbox[c]{2.75in}{
\begin{center}\centerline{
\includegraphics[width=2.5in]{images/mulv_tabs.pdf}}
\end{center}
}
+To delete a view, press [CTRL]-W (or [CMD]-W (Mac)).
+To rename a view, right click the view's name, this open the Enter View Name dialogue box, enter the desired name.
% JBPNote make an excercise on views ?
\subsection{Alignment Layout}
-Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped, where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
+Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped,
+where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the
+alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
\subsubsection{Wrapped Alignments}
-Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation lines are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when working with large numbers of sequences.
+Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that
+the annotation tracks are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when
+working with large numbers of sequences.
-If annotations are not all visible in wrapped mode, expand the alignment window to view them. Note that alignment annotation (see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult.
+If annotations are not all visible in wrapped mode, expand the alignment window to view them. Note that alignment annotation
+(see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult.
\begin{figure}[htbp]
\begin{center}
\parbox[c]{2in}{\includegraphics[width=2in]{images/wrap1.pdf}}
\subsubsection{Fonts}
-\parbox[c]{4in}{The text appearance in a view can be modified {\sl via} the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
+\parbox[c]{4in}{The text appearance in a view can be modified {\sl via} the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting
+applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by
+clicking the middle mouse button and dragging across the alignment window.}
\parbox[c]{2in}{\centerline{\includegraphics[width=1.75in]{images/font.pdf}}}
\subsubsection{Numbering and Label Justification}
-Options in the {\sl Format} menu are provided to control the alignment view, and provide a range of options to control the display of sequence and alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
+Options in the {\sl Format} menu are provided to control the alignment view, and provide a range of options to control the display of sequence and
+alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
\subsubsection{Alignment and Group Colouring and Appearance}
-The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Hidden Markers} and {\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.
+The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Show Hidden Markers} and
+{\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.
\subsubsection{Highlighting Nonconserved Symbols}
The alignment layout and group sub-menu both contain an option to hide
display gaps or sequence symbols that differ from the consensus for each
column, and render all others with a `.'.
%TODO add a graphic to illustrate this.
+
\subsection{Annotation Ordering and Display}
% TODO: describe consensus, conservation, quality user preferences, and group
% annotation preferences.
The annotation lines which appear below the sequence alignment are described in
-detail in Section \ref{featannot}. They can be hidden by toggling the {\sl View
-$\Rightarrow$ Show Annotations} menu option. Additionally, each annotation line
+detail in Section \ref{featannot}. They can be hidden by toggling the {\sl Annotations
+$\Rightarrow$ Show annotations} menu option. Additionally, each annotation line
can be hidden and revealed in the same way as sequences {\sl via} the
pop-up context menu on the annotation name panel (Figure \ref{annot}).
Annotations can be reordered by dragging the annotation line label on the annotation label panel. Placing the
mouse over the top annotation label brings up a resize icon on the left. When this is
-displayed, Click-dragging up and down provides more space in the alignment window for viewing the annotations, and less space for the sequence alignment.
+displayed, click-dragging up and down provides either more space in the alignment window for viewing the annotations, or
+less space for the sequence alignment.
\begin{figure}
\begin{center}
\includegraphics[width=2.5in]{images/annot1.pdf}
\includegraphics[width=2.5in]{images/annot2.pdf}
\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl
-View} menu (left) or individually from the context menu (right).}
+Annotations} menu (left) or individually from the context menu opened by right clicking their label (right).}
\label{annot}
\end{center}
\end{figure}
-\exercise{Alignment Layout}{
-\label{exscreen}
-\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}.
-Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
-Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
-sequence ID format and so on. }
-\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 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 on the sequence name and
-dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
-\exstep{Move the mouse to the top left hand corner of the annotation labels -
-a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
-by clicking and dragging this icon up or down.}
-\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+%%TODO: multiple views - simple edits - observe changes in other views.
+
\subsection{Graphical Output}
\label{figuregen}
-\parbox[c]{4in}{Jalview allows alignments figures to be exported in three different formats, each of which is suited to a particular purpose. Image export is {\sl via} the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ \ldots } alignment window menu option. }
-\parbox[c]{2in}{\centerline{\includegraphics[width=1.25in]{images/image.pdf}}}
+\parbox[c]{4in}{Jalview allows alignments figures to be exported in different formats, each of which is suited to a particular purpose.
+Image export is {\sl via} the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ \ldots } alignment window menu option. }
+\parbox[c]{2in}{\centerline{\includegraphics[width=2in]{images/image.pdf}}}
\subsubsection{HTML}
-\parbox[c]{3in}{HTML is the format used by web pages. Jalview outputs the alignment as an HTML table with all the colours and fonts as seen. Any additional annotation will also be embedded as sensitive areas on the page, such as URL links for each sequence's ID label. This file can then be viewed directly with any web browser. Each residue is placed in an individual table cell. Unwrapped alignments will produce a very wide page.}
+\parbox[c]{4in}{HTML is the format used by web pages. Jalview outputs the
+alignment as a 'Scalable Vector Graphics' (or SVG) file with all the colours and fonts as seen, which is in turn embedded as a
+scrollable component within an HTML page.
+%% Functionality lost in 2.9 Any additional annotation will also be embedded as sensitive areas on the page, such as URL links for each sequence's ID label.
+This file can then be viewed directly with any web browser. Unwrapped alignments will produce a very wide page. Export options allow
+original data to be embedded in the HTML file as BioJSON.\footnote{BioJSON was introduced in Jalview 2.9 and fully described
+at \url{https://jalview.github.io/biojson/}}}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_html.pdf}}}
\subsubsection{EPS}
-\parbox[c]{3in}{EPS is Encapsulated Postscript. {\bf It is the format of choice
+\parbox[c]{4in}{EPS is Encapsulated Postscript. {\bf It is the format of choice
for publications and posters} as it gives the highest quality output of any of
the image types. It can be scaled to any size, so will still look good on an A0
poster.
This format can be read by most good presentation and graphics packages such as Adobe Illustrator or Inkscape.
}
-\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_eps.pdf}} \par \centerline{Zoom Detail of EPS image.}}
+\parbox[c]{4in}{\centerline{\includegraphics[width=2in]{images/image_eps.pdf}}
+\par \centerline{Zoom Detail of EPS image.}}
\subsubsection{PNG}
-\parbox[c]{3in}{
-PNG is Portable Network Graphics. This output option produces an image that can be easily included in web pages and incorporated in presentations using e.g. Powerpoint or Open Office. It is a bitmap image so does not scale and is unsuitable for use on posters, or in publications.
+\parbox[c]{4in}{
+PNG is Portable Network Graphics. This output option produces an image that can be easily included in web pages and incorporated in
+presentations using e.g. Powerpoint or Open Office. It is a bitmap image so does not scale and is unsuitable for use on posters,
+or in publications.
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.}}
+\parbox[c]{4in}{\centerline{\includegraphics[width=2in]{images/image_png.pdf}}
+\par \centerline{Zoom Detail of PNG image.}}
\exercise{Graphical Output}{
\label{graphicex}
$\Rightarrow$ 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.}
+\exstep{Experiment with Jalview's other output options: try exporting an alignment view as 'BioJS', which employs the BioJS Multiple Sequence Alignment viewer. When would you use this type of export option ?}
+\exstep{Working with embedded BioJSON data. Drag and drop (or load via the file browser) the 'BioJS' HTML file in the previous step. Compare the original and imported alignment views - are there differences ?}
\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.
}
but are shown mapped on to specific residues within the alignment.
Features and annotation can be interactively created, or retrieved from external
-data sources. Webservices like JPred (see \ref{jpred} above) can be used to
+data sources. Webservices like JPred (see \ref{jpred}) can be used to
analyse a given sequence or alignment and generate annotation for it.
-\section{Conservation, Quality and Consensus Annotation}
+\section{Conservation, Quality, Consensus and other Annotation}
\label{annotationintro}
Jalview automatically calculates several quantitative alignment annotations
which are displayed as histograms below the multiple sequence alignment columns.
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{Occupancy Annotation}
+
+Alignment occupancy simply reflects the number of residues aligned at each column
+in the multiple sequence alignment. To see this annotation you may first need to enable it by ticking the {\sl Occupancy} check-box
+in the {\sl Visual} tab in Jalview's {\sl Preferences} before opening an alignment. Occupancy is particularly useful in conjunction with
+the {\sl Select/Hide by Annotations} dialog since it allows the view to be filtered to exclude regions of the alignment with a high proportion of gaps.
+
\subsubsection{Group Associated Annotation}
\label{groupassocannotation}
Group associated consensus and conservation annotation rows reflect the
Right-click on the label name of the {\sl Conservation} annotation row to
bring up the context menu and select {\sl Add New Row}. A dialog box will
appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
-Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
+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.
+"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
+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
+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
+ 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.
}
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
+(The format for this file is given in the Jalview help. Press [F1] to open it ([F1]-[Fn] (Mac)),
+and find the "Annotations File Format" entry in the "Alignment Annotations" section of the contents
pane.) }
\exstep{Open a text editor and copy the annotation text into the editor.
along the row, save the file and re-importing it into Jalview as previously.
{\sl Hint: Use the Export Annotation function to view what helix annotation looks like in
a Jalview annotation file.}}
-\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
-function to export all the alignment's annotation to a file. Save the file.}
+\exstep{In the alignment window menu, select {\sl File $\Rightarrow$ Export Annotations...}
+to export all the alignment's annotation to a file. Save the file.}
\exstep{Open the exported annotation in a text editor, and use the Annotation File Format
documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
they appear as several lines on a single line graph.
Recover or recreate the secondary structure predictions that you made from
JPred. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row.
-
Note: the
SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
annotation.
\url{http://www.jalview.org/training/Training-Videos}.}
+\section{Sequence Features}
+Sequence features are annotation associated with a specific sequence - often marking a specific region, such as a domain or binding site. Jalview allows features to 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}
+\includegraphics[width=2in]{images/feature1.pdf}
+\includegraphics[width=2.5in]{images/feature2.pdf}
+\includegraphics[width=1.5in]{images/feature3.pdf}
+\caption{{\bf Creating sequence features.} Features can readily be created from selections via the context menu and are then displayed on the sequence. }
+\label{features}
+\end{center}
+\end{figure}
+
+Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence.
+Each feature remains associated with its own sequence.
+
+%%TODO: change EMBL to ENA in Jalview and the Manual !
+
\section{Importing Features from Databases}
\label{featuresfromdb}
Jalview supports feature retrieval from public databases.
-It includes built in parsers for Uniprot and ENA (or EMBL) records retrieved
+It includes built in parsers for Uniprot, Ensembl 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.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=4in]{images/features4.pdf}
+\caption{{\bf Multiple sequence features.} An alignment with JPred secondary structure prediction annotation below it, and many sequence features overlaid onto the aligned sequences. The tooltip lists the features annotating the residue below the mouse-pointer.}
+\end{center}
+\end{figure}
+
+
\subsection{Sequence Database Reference Retrieval}
\label{fetchdbrefs}
Jalview maintains a list of external database references for each sequence in
You can export all the database cross references and annotation terms shown in
the sequence ID tooltip for a sequence by right-clicking and selecting the {\sl
-[Sequence ID] $\Rightarrow$ Sequence details \ldots} option from the popup
+[Sequence ID] $\Rightarrow$ Sequence Details} option from the popup
menu.
A similar option is provided in the {\sl Selection} sub-menu allowing you to
obtain annotation for the sequences currently selected.
Jalview includes a function to automatically verify and update each sequence's
start and end numbering against any of the sequence databases that the {\sl
Sequence Fetcher} has access to. This function is accessed from the {\sl
-Webservice $\Rightarrow$ Fetch DB References} sub-menu in the Alignment
+Web Service $\Rightarrow$ 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, or just a specific datasource from one of the submenus.
+Databases}, which includes EMBL, Ensembl, 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
{\sl ``Sequence not 100\% match'' dialog box}).
-\subsubsection{The Fetch Uniprot IDs Dialog Box}
-\label{discoveruniprotids}
-If any sources are selected which refer to Uniprot coordinates as their reference system,
-then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing OK instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Service $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}.
-If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record.
-
\subsubsection{Rate of Feature Retrieval}
Feature retrieval can take some time if a large number of sources are selected
and if the alignment contains a large number of sequences.
The retrieved features are shown on the sequence and can be customised as described previously.
-\subsection{Colouring Features by Score or Description
-Text}
+\subsection{Customising Feature Display}
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5in]{images/features5.pdf}
+\caption{{\bf Customising sequence features.} Features can be recoloured, switched on or off and have the rendering order changed. }
+\label{custfeat}
+\end{center}
+\end{figure}
+
+Feature display can be toggled on or off by selecting the {\sl View
+$\Rightarrow$ Show Sequence Features} menu option. When multiple features are
+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 dialog window (Figure \ref{custfeat}) which allows the
+visibility of individual feature types to be selected, assigned colours to be 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
+slider alters the transparency of the feature rendering. Clicking in the {\sl Configuration} column
+ opens the {\sl Display Settings} dialog which allows more complex shading schemes
+ and also the creation of filters, and right-clicking opens a context sensitive menu
+ that offers options for selecting and hiding columns or sorting the alignment according the feature's distribution or score attribute.
+These capabilities are described further in sections
+\ref{featureschemes} and \ref{featureordering}.
+
+
+\subsection{Changing how Features are coloured and displayed}
\label{featureschemes}
Sometimes, you may need to visualize the differences in information carried by
sequence features of the same type. This is most often the case when features
-of a particular type are the result of a specific type of database query or calculation. Here, they may also carry information within their textual description, or most commonly for calculations, a score related to the property being investigated. Jalview can shade sequence
-features using a graduated colourscheme in order to highlight these variations.
-In order to apply a graduated scheme to a feature type, select the `Graduated
-colour' entry in the Sequence {\sl Feature Type}'s popup menu, which is opened by
-right-clicking the {\sl Feature Type} or {\sl Color} in the {\sl Sequence Feature Settings} dialog box. Two types
-of colouring styles are currently supported: the default is quantitative
-colouring, which shades each feature based on its score, with the highest
-scores receiving the `Max' colour, and the lowest scoring features coloured
-with the `Min' colour. Alternately, you can select the `Colour by label'
+of a particular type are the result of a specific type of database query or calculation.
+Here, they may also carry information within their textual description, or most commonly
+for calculations, a score related to the property being investigated. Features imported
+from genomic databases and Variant Call Format files may also have a number of additional
+attributes. Jalview allow filters and different types of colouring to be applied to allow variations in these attributes to be highlighted.
+In order to create a filter or modify the way a feature type is coloured, select the `Configuration' column for that {\sl Feature Type} in the {\sl Sequence Feature Settings} dialog box.
+
+Instead of shading a feature with an assigned colour according to its type, you can select the `Colour by text'
option to create feature colours according to the description text associated
with each feature. This is useful for general feature types - such as
Uniprot's `DOMAIN' feature - where the actual type of domain is given in the
-feature's description.
+feature's description. If other attributes are present you can choose one of them from the drop-down menu.
-Graduated feature colourschemes can also be used to exclude low or
+If Scores or numeric attributes are present, the {\sl Graduated Colour} section of the dialog allows a quantitative
+shading scheme to be defined, with the highest
+scores receiving the `Max' colour, and the lowest scoring features coloured
+with the `Min' colour. Alternately,
+you can define a threshold to exclude low or
high-scoring features from the alignment display. This is done by choosing your
desired threshold type (either above or below), using the drop-down menu in the
dialog box. Then, adjust the slider or enter a value in the text box to set the
threshold for displaying this type of feature.
-The feature settings dialog box allows you to toggle between a graduated and
-simple feature colourscheme using the pop-up menu for the feature type. When a
-graduated scheme is applied, it will be indicated in the colour column for
-that feature type - with coloured blocks or text to indicate the colouring
-style and a greater than ($>$) or less than ($<$) symbol to indicate when a
-threshold has been defined.
+When a filters and complex colourschemes are applied, the configuration column will show coloured blocks or text to indicate the colouring
+style and any attribute filters.
+
\subsection{Using Features to Re-order the Alignment}
\label{featureordering}
The presence of sequence features on certain sequences or in a particular
region of an alignment can quantitatively identify important trends in
the aligned sequences. In this case, it is more useful to
-re-order the alignment based on the number of features or their associated scores, rather than simply re-colour the aligned sequences. The sequence feature settings
-dialog box provides two buttons: `Seq sort by Density' and `Seq sort by
+re-order the alignment based on the number of features or their associated scores, rather than simply re-colour the aligned sequences.
+The sequence feature settings
+dialog box provides two buttons: `Sequence sort by Density' and `Sequence sort by
Score', that allow you to reorder the alignment according to the number of
sequence features present on each sequence, and also according to any scores
associated with a feature. Each of these buttons uses the currently displayed
% colour styles are encoded. }
% }
-\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 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}
-\includegraphics[width=2in]{images/feature1.pdf}
-\includegraphics[width=2.5in]{images/feature2.pdf}
-\includegraphics[width=1.5in]{images/feature3.pdf}
-\caption{{\bf Creating sequence features.} Features can readily be created from selections via the context menu and are then displayed on the sequence. }
-\label{features}
-\end{center}
-\end{figure}
-
-Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence.
-Each feature remains associated with its own sequence.
-
-\subsection{Customising Feature Display}
-
-Feature display can be toggled on or off by selecting the {\sl View
-$\Rightarrow$ Show Sequence Features} menu option. When multiple features are
-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 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
-slider alters the transparency of the feature rendering. The Feature
-Settings dialog also includes functions for more advanced feature shading
-schemes and buttons for sorting the alignment according to the distribution of
-features. These capabilities are described further in sections
-\ref{featureschemes} and \ref{featureordering}.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=4in]{images/features4.pdf}
-\caption{{\bf Multiple sequence features.} An alignment with JPred secondary structure prediction annotation below it, and many sequence features overlaid onto the aligned sequences. The tooltip lists the features annotating the residue below the mouse-pointer.}
-\end{center}
-\end{figure}
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=4in]{images/features5.pdf}
-\caption{{\bf Customising sequence features.} Features can be recoloured, switched on or off and have the rendering order changed. }
-\label{custfeat}
-\end{center}
-\end{figure}
\subsection{Sequence Feature File Formats}
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.
+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 using the [SHIFT] key.
Roll the mouse over the features and you will see that the feature has moved
with the sequence. Delete the gap you created using {\sl Edit
$\Rightarrow$ Undo}.
feature type is now turned off. Click it again and note that the features are
now displayed. Close the sequence feature settings box by clicking {\sl OK} or
{\sl Cancel}.}
+
+\exstep{Select {\sl View $\Rightarrow$ Show Sequence Features} from the
+alignment window menu. The sequence features are now hidden. Repeat this step and the features are
+displayed.}
+
\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
\exercise{Multiple Sequence Alignment}{
\label{msaex}
-\exstep{ Close all windows and open the alignment at {\sf
+\exstep{ Close all windows. 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
+ the window, and repeat using {\sl ClustalO} (Omega) ({\sl with Defaults}), 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
+\exstep{Select the last three sequences in the MAFFT alignment (you may need the scroll down the 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
\begin{figure}[htbc]
\center{
\includegraphics[width=3in]{images/jvaliwsparamsbox.pdf}
-\caption{{\bf Jalview's JABA alignment service parameter editing dialog box}.}
+\caption{{\bf An alignment service's parameter editing dialog box}.}
\label{jwsparamsdialog} }
\end{figure}
Each parameter available for a method usually has a short description, which
Jalview will display as a tooltip, or as a text pane that can be opened under
the parameter's controls. In the parameter shown in Figure
-\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
-service can also be accessed, by right clicking the button and selecting a URL
-from the pop-up menu that will open.
+\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side.
\begin{figure}[htbp]
\begin{center}
it will show your custom preset amongst the options available for running the
JABA service.
+%% TODO - reinstate this exercise about reinstating presets
%
% \exercise{Creating and using user defined presets}{\label{createandusepreseex}
% \exstep{Import the file at
% }
% }
+%%TODO just typing a value into parameter slider doesn't actually modify value, return needs to be hit. This is not intuitive (these days) - loss of focus should update values of parameters (e.g. when the run/start job button is hit)
+
\section{Protein Alignment Conservation Analysis}
\label{aacons}
The {\sl Web Service $\Rightarrow$ Conservation} menu controls the computation
-of up to 17 different amino acid conservation measures for the current alignment
+of over 17 different amino acid conservation measures for the current alignment
view. The JABAWS AACon Alignment Conservation Calculation Service, which is used
to calculate these scores, provides a variety of standard measures described by
Valdar in 2002\footnote{Scoring residue conservation. Valdar (2002) {\sl
If you are working with alignments too large to analyse with the public JABAWS
server, then you will most likely have already configured additional JABAWS
servers. By default, Jalview will chose the first AACon service available from
-the list of JABAWS servers available. If available, you can switch to use
-another AACon service by selecting it from the {\sl Web Service $\Rightarrow$
-Conservation $\Rightarrow$ Switch Server} submenu.
+the list of JABAWS servers available. You can change the AACon services by
+selecting it from the {\sl Web Service $\Rightarrow$
+Conservation $\Rightarrow$ Change AACon Settings} submenu.
+Alternatively to add new service, go to the desktop window menu and select {\sl Tools $\Rightarrow$
+Preferences $\Rightarrow$ Web Services tab} and add {\sl New Services URL}, then use the {\sl move up} or {\sl move down} buttons
+to reorder the services.
+
\chapter{Analysis of Alignments}
\label{alignanalysis}
alignment window menu. Computationally intensive analyses are run outside
Jalview {\sl via} web services - and found under the
{\sl Web Service} menu. In this section, we describe the built-in analysis
-capabilities common to both the Jalview Desktop and the JalviewLite applet.
+capabilities common to both the Jalview Desktop and the JalviewJS.
\section{PCA}
Principal components analysis calculations create a spatial
position between each pair of sequences. The basic method is described in the
1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl
Nature Structural Biology} (1995) {\bf 2}, 171-8.
-PMID: 7749921} and implemented at the SeqSpace server at the EBI.
-
-Jalview provides two different options for the PCA calculation: SeqSpace and
-Jalview mode. In SeqSpace mode, PCAs are computed using the identity matrix, and
-gaps are treated as 'the unknown residue' (this actually differs from the
-original SeqSpace paper, and will be adjusted in a future version of Jalview).
-In Jalview mode, PCAs are computed using the chosen score matrix - which for
-protein sequences, defaults to BLOSUM 62, and for nucleotides, is the
-DNA identity matrix that also treats Us and Ts as identical, to support analysis
-of both RNA and DNA alignments. The {\sl Change Parameters} allows the
-calculation method and score models to be changed.\footnote{See
-\url{http://www.jalview.org/help/html/calculations/pca.html}.}
+PMID: 7749921} and implemented at the SeqSpace server at the EBI.\footnote{See \url{http://www.jalview.org/help/html/calculations/pca.html}.}
+%
+% Jalview provides two different options for the PCA calculation: SeqSpace and
+% Jalview mode. In SeqSpace mode, PCAs are computed using the identity matrix, and
+% gaps are treated as 'the unknown residue' (this actually differs from the
+% original SeqSpace paper, and will be adjusted in a future version of Jalview).
+% In Jalview mode, PCAs are computed using the chosen score matrix - which for
+% protein sequences, defaults to BLOSUM 62, and for nucleotides, is the
+% DNA identity matrix that also treats Us and Ts as identical, to support analysis
+% of both RNA and DNA alignments.
\subsubsection{The PCA Viewer}
-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}).
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Tree or PCA} menu option.
+{\bf PCA requires a selection containing at
+least 4 sequences}. In the Choose Calculation window, select the {\sl Principal Components Analysis} button and then select {\sl Calculate}
+(Figure \ref{PCA}).
Each sequence is represented by a small square, coloured by the background
colour of the sequence ID label. The axes can be rotated by clicking and
dragging the left mouse button and zoomed using the $\uparrow$ and $\downarrow$
[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
+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.
+the {\sl File $\Rightarrow$ Save as $\Rightarrow$ \ldots } submenu.
\exercise{Principal Component Analysis}
{\label{pcaex}
\section{Trees}
\label{trees}
+
Jalview can calculate and display trees, providing interactive tree-based
grouping of sequences though a tree viewer. All trees are calculated {\sl via}
-the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu.
+the {\sl Calculate $\Rightarrow$ Tree or PCA \ldots} menu option.
Trees can be calculated from distance matrices determined from \% identity or
aggregate BLOSUM 62 score using either {\sl Average Distance} (UPGMA) or {\sl
Neighbour Joining} algorithms. The input data for a tree is either the selected
- unmatched leaves will still be displayed, and can be highlighted using the
{\sl View $\Rightarrow$ Mark Unlinked Leaves} menu option.
+
+
+\begin{figure}
+\begin{center}
+\includegraphics[width=2.5in]{images/trees1.pdf}
+\includegraphics[width=2.5in]{images/trees2.pdf}
+\includegraphics[width=1.25in]{images/trees4.pdf}
+\caption{{\bf Calculating Trees} Jalview provides a range of options
+for calculating trees.
+Jalview can also load precalculated trees in Newick format (right).}
+\label{trees1}
+\end{center}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+\includegraphics[width=5in]{images/trees3.pdf}
+\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
+groups in Jalview.}
+\label{trees2}
+\end{center}
+\end{figure}
+
+Clicking on the tree brings up a cursor across the height of the tree. The
+sequences are automatically partitioned and coloured (Figure \ref{trees2}). To
+group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
+By Tree Order $\Rightarrow$ \ldots} alignment window menu option and choose the
+correct tree. The sequences will then be sorted according to the leaf order
+currently shown in the tree view. The coloured background to the sequence IDs
+can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the
+alignment window menu. Note that tree partitioning will also remove any groups
+and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to
+preserve these.
+
+
\exercise{Trees}
{\label{treeex}
-{\sl Ensure that you have at least 1G memory available in Jalview.
-(Start with link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
-or in the table in the Development section of the Jalview web site
-(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds}), go
-to ``latest official build'' row and in the ``Webstart'' column, click
-on ``2G''.)}
\exstep{Open the alignment at
\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
-window and a dialogue box opens. In the tree section select Neighbour
+window menu and a dialogue box opens. In the tree section select Neighbour
Joining, in the drop-down list select BLOSUM62 and click the Calculate
button. A tree window will open.}
\exstep{Click on the
-tree window, a cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour.
-Place the cursor to give about 4 groups.}
+tree window, a cursor will appear as a vertical line. Note that clicking will
+place this cursor, and divides the tree into a number of groups, each highlighted
+with a different colour. Place the cursor to give about 4 groups.}
+\exstep{Place the mouse cursor on a node of the tree to open a tool tip. Double click the node to invert the leaves.
+}
\exstep{In the tree window, select {\sl View $\Rightarrow$ Sort Alignment
by Tree}. The sequences are reordered to match the order in the tree and groups
tree window will appear. The group colouring makes it easy to see the differences between the two
trees calculated by the different methods.}
-\exstep{In the alignment window, select sequence 2 from
+\exstep{With no groups selected in the alignment window, select sequence 2 from
column 60 to sequence 12 and column 123. Select {\sl Calculate $\Rightarrow$
Tree or PCA..}. , in the dialogue box select Neighbour Joining and
BLOSUM62, then click the Calculate button.
}
-\begin{figure}
-\begin{center}
-\includegraphics[width=2.5in]{images/trees1.pdf}
-\includegraphics[width=2.5in]{images/trees2.pdf}
-\includegraphics[width=1.25in]{images/trees4.pdf}
-\caption{{\bf Calculating Trees} Jalview provides a range of options
-for calculating trees.
-Jalview can also load precalculated trees in Newick format (right).}
-\label{trees1}
-\end{center}
-\end{figure}
-
-
-Clicking on the tree brings up a cursor across the height of the tree. The
-sequences are automatically partitioned and coloured (Figure \ref{trees2}). To
-group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
-By Tree Order $\Rightarrow$ \ldots} alignment window menu option and choose the
-correct tree. The sequences will then be sorted according to the leaf order
-currently shown in the tree view. The coloured background to the sequence IDs
-can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the
-alignment window menu. Note that tree partitioning will also remove any groups
-and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to
-preserve these.
-
-\begin{figure}
-\begin{center}
-\includegraphics[width=5in]{images/trees3.pdf}
-\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
-groups in Jalview.}
-\label{trees2}
-\end{center}
-\end{figure}
-
%\subsubsection{Multiple Views and Input Data recovery from PCA and Tree Viewers}
% move to ch. 3 ?
%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
better understand the pattern of similarity revealed by the tree and the
variation within the clades partitioned by the grouping. The conservation based
colourschemes and the group associated conservation and consensus annotation
-(enabled using the alignment window's {\sl View $\Rightarrow$ Autocalculated
+(enabled using the alignment window's {\sl Annotations $\Rightarrow$ Autocalculated
Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
can help when working with larger alignments.
\subsection{Redundancy Removal}
-The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented by a chosen sequence, rather than deleted.}.
+The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option
+in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function,
+but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity
+slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater
+than the current threshold are highlighted in black. The [Remove] button can then be used to delete these
+sequences from the alignment as an edit operation.
\begin{figure}
\begin{center}
\includegraphics[width=5.5in]{images/redundancy.pdf}
\end{center}
\label{removeredundancydialog}
-\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.}
+\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}
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
+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.}
+\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 {\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
+create a new view. Ensure the annotation panel is displayed ({\sl Annotations $\Rightarrow$ Show Annotations} is toggled on). 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.}
+Autocalculated Annotation $\Rightarrow$
+Group Consensus} submenu.}
+
\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.
+group. Activate the logo by right clicking the name of the Consensus annotation to
+open the context menu and select the {\sl Show Logo} option. Alter its size, by moving the cursor onto the annotation row, right clicking the
+mouse and dragging it up. Alter its position, by right clicking the name of the Consensus annotation
+and dragging it up to the top of the annotations.}
+\exstep{In the column alignment ruler, select a column exhibiting with about 50\%
+ of its residues conserved ({\em ie. about 50\% in the consensus histogram})
+ 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}.}
+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 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
\subsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
Match}
\label{multipdbfileassoc}
-If you have PDB files stored on your computer named the same way as the
-sequences in the alignment, then you can drag them from their location on the
+If you have PDB files stored on your computer {\bf named the same way as the
+sequences in the alignment}, then you can drag them from their location on the
file browser onto an alignment window. Jalview will search the alignment for
sequences with IDs that match any of the files, and offer a dialog like the one
in Figure \ref{multipdbfileassocfig}.
sequence within a local directory. Check out
\href{http://issues.jalview.org/browse/JAL-801}{Jalview issue 801}}
-After associating sequences with PDB files, you can view the PDB structures by
+After associating sequences with PDB files, you can view the PDB structures by
opening the Sequence ID popup
menu and selecting {\sl View 3D Structure}. The PDB files you loaded will be
shown in the {\bf Cached Structures} view, after selecting it from the drop down
The structure(s) to be displayed will be downloaded or loaded from
the local file system, and shown as a ribbon diagram coloured according to the
-associated sequence in the current alignment view (Figure \ref{structure}
-(right)). The structure can be rotated by clicking and dragging in the structure
+associated sequence in the current alignment view (Figure \ref{structure}). The structure can be rotated by clicking and dragging in the structure
window. The structure can be zoomed using the mouse scroll wheel or by
[SHIFT]-dragging the structure.
automatic application of colour schemes when new structure data is added, or
when associated alignment views are modified.
+%%TODO: no mapping when using N&W alg.
+
\exercise{Viewing Structures with the integrated Jmol Viewer}{
\label{viewingstructex}
\exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar}.}
+\textsf{http://www.jalview.org/examples/exampleFile.jvp}.}
\exstep{Right-click on the
sequence ID label of {\sl FER1\_SPIOL} to open
-the ID popup menu and select {\sl 3D Structure}. After a short pause, a
+the ID popup menu and select {\sl 3D Structure Data}. After a short pause, a
Structure Chooser dialog will open for the sequence, listing available
-structure data from the PDB. Select { \sl 1A70} from the list and click {\sl
-View}.
+structure data from the PDB. Select { \sl 1a70} from the list and click {\sl
+New View}.
-{\sl The Structure Chooser dialog presents available PDB structures
+{\sl Note:} The Structure Chooser dialog presents available PDB structures
by querying the EMBL-EBI's PDBe web API. Extra information can be
-including in this window by checking boxes in the columns of the ``Customise Displayed Options'' tab}.
+including in this window by checking boxes in the columns of the {\sl Customise Displayed Options} tab.
% JBP Note: Bug JAL-1238 needs to be fixed ASAP
}
\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
+\exstep{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{Roll the
+mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment window.
+If a residue in the sequence maps to one in the structure, the residue molecular shape is visible in the structure viewer.}
\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. }
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.
+\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.
+\exstep{In the structure window, select {\sl File $\Rightarrow$ Save as $\Rightarrow$ PDB file} and enter a filename to save the PDB file.
+Once the file is saved, open the location in your file browser and drag the PDB file that you just saved onto the Jalview desktop.
+(Or load it from the Jalview Desktop menu using
+{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File}).
+Verify that you can open and view the associated structure from new alignment window using the sequence ID
+context menu's {\sl 3D Structure } submenu (as step {\sl b)}.}
+
+\exstep{In the Jmol window, right click on the background to open the
+Jmol menu options. Explore this, for example by
+{\sl Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected),
+and then the {\sl 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 (jvp). 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}.}
\exstep{Continue with the Jalview project created in exercise
\ref{viewingstructex}}
-\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL
-by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$
-3D Structure Data \ldots } }
+\exstep{Select the FER1\_MAIZE sequence (near bottom of the alignment). Right-click the ID label to open the context menu,
+select {\sl $\Rightarrow$ 3D Structure Data}.}
-\exstep{Pick 1A70 from the Structure Chooser dialog, and click the {\bf View}
-button. Jalview will give you the option of aligning the
-structure to the one already open. To superimpose the structure associated with
-FER1\_MAIZE with the one associated with FER1\_SPIOL, press {\sl Yes}.
+\exstep{This opens the Structure Chooser dialog, pick 1gaq from the list.
+Make sure the {\sl Superpose} option is checked before clicking the {\bf Add}
+button. This superimpose the structure associated with
+FER1\_MAIZE with the one associated with FER1\_SPIOL.
-{\sl The Jmol view should update to show both structures, and one will be
+{\sl Note:} The Jmol view should update to show both structures, and one will be
moved on to the other. If this doesn't happen, use the Align function in the
-Jmol submenu}.
+Jmol submenu.
}
-\exstep{Create a new view on the alignment, and hide all but columns 121
-through to 132 (you can do this via {\sl View $\Rightarrow$ Hide $\Rightarrow$
+\exstep{Create a new view on the alignment ({\sl View $\Rightarrow$ New View}), and hide all but columns 121
+through to 132 ({\sl View $\Rightarrow$ Hide $\Rightarrow$
All but selected region}).}
-\exstep{Select the newly created view in the {\sl Jmol $\Rightarrow$ Superpose
+\exstep{Select the newly created view in the structure window using {\sl Jmol $\Rightarrow$ Superpose
With } submenu, and then recompute the superposition with {\sl Jmol
-$\Rightarrow$ Align Structures}.
+$\Rightarrow$ Superpose Structures}.
-{\sl Note how the molecules shift position when superposed with only a small
-region of the alignment.}}
+{\sl Note:} how the molecules shift position when superposed with only a small
+region of the alignment.}
\exstep{Compare RMSDs obtained when superimposing molecules with
-columns 121-132 and with the whole alignment.}
-
-\exstep{The RMSD report can be
+columns 121-132 and with the whole alignment. The RMSD report can be
viewed by right clicking the mouse on Jmol window, and select {\sl
Console} from the menu (if nothing is shown, recompute the superposition after
-displaying the console).
-
-Which view do you think give the best 3D superposition, and why ?} }
+displaying the console).}
+\exstep{Which view do you think give the best 3D superposition, and why ?} }
\exercise{Setting Chimera as the default 3D Structure Viewer}{
\label{viewingchimera}
\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
+If this does not work then you may need to set the {\sl Path to Chimera program} in {\sl Preferences}.
+{\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.}
+view window sits inside the Jalview desktop.
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}}
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
+correspondences defined by one or more sequence alignments involving structures shown in the Jmol display.
+Superposition based on the currently displayed alignment view
happens automatically if a
structure is added to an existing Jmol display using
the {\sl 3D Structure } option in the Sequence ID popup menu to open the
\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 1G of
-free memory available.
-{\sl See section \ref{memorylimits} for how to do this or click the following
-link:
-
-\url{http://www.jalview.org/services/launchApp?jvm-max-heap=2G} }}
\exstep{Retrieve the following PFAM alignments from the {\bf PFAM (full)} source
:
-PF02008 PF01426 PF00145 (enter all three - they
-will each be retrieved into their own alignment window).}
+PF02008; PF01426; PF00145 (retrieve each into their own alignment window).}
\exstep{Drag the URL or file of the structure you
downloaded in step 1 onto one of the alignments to associate it with the mouse sequence in that Pfam domain family.}
\exstep{Locate every DNMT1\_MOUSE sequence in the
alignment by opening the Find dialog box via {\sl Select
-$\Rightarrow$ Find}. Search using the text DNMT1\_MOUSE. For
-each one, open the Structure Chooser dialog box by right clicking the mouse on
+$\Rightarrow$ Find}. Search using the text DNMT1\_MOUSE. Open the Structure Chooser dialog box
+by right clicking the mouse on
sequence name to open the context menu and select {\sl
$\Rightarrow$ 3D Structure Data}.
Select `Cached Structures' from
-the drop-down menu in the Structure Chooser dialog box, select the
-DNMT1\_MOUSE.pdb structure, and click {\bf View}.
+the drop-down menu in the Structure Chooser dialog box and select the
+DNMT1\_MOUSE.pdb structure, and click {\sl New View}.
{\em Part of the newly opened structure will be coloured the same way as
the associated DNMT1\_MOUSE sequence is in the alignment view.}
!} {\em This will cause Jalview to attempt to discover all structures for
sequences in the alignment.}
}
-\exstep{Repeat the previous two steps for each of the other
-alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and
-hitting the `View' button on the Structure Chooser dialog. Jalview will ask if
-you wish to create a new Jmol view, respond {\bf `Yes'} each time. This will
-ensure each sequence fragment is associated with the {\bf same} Jmol view. }
+\exstep{Repeat the previous two steps for the other two
+ alignments. For those, after selecting the DNMT1\_MOUSE.pdb structure you
+ should select {\bf `Add'} to ensure each domain alignment is associated
+ with the {\bf same} Jmol view. }
\exstep{Pick a different
-colourscheme for each alignment, and use the {\sl Colour by ..} submenu to
-ensure they are all used to colour the complex shown in the Jmol window.
-
-{\sl The different shading schemes will allow regions of strong physicochemical conservation are
-highlighted on the domains in the structure.}
+colourscheme in each alignment window for each alignment using the {\sl Colour $\Rightarrow$ Colour by...} submenu to
+ensure each of the complexes shown in the Jmol window are coloured.
+{\sl The different shading schemes will highlight regions of strong
+physicochemical conservation on corresponding domains in the structure.}
}
\exstep{The final step needed to reproduce the shading in Figure
{\bf Conservation} annotation row (introduced in section
\ref{colourbyannotation}).
-Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu
+{\sl Note:} Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu
option, or you may not see any colour changes in the associated structure.
{\sl Examine the regions strongly coloured at the interfaces between each
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
-{\sl Note: The annotation panel can get quite busy during this exercise. Try
+{\sl Note:} The annotation panel can get quite busy during this exercise. Try
hiding some annotations rows by right clicking
the mouse in the annotation label panel and select the ``Hide this row'' option.
The Annotations dropdown menu on the alignment window also provides options for
-reordering and hiding autocalculated and sequence associated annotation. }
+reordering and hiding autocalculated and sequence associated annotation.
\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by
clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$
Secondary Structure Prediction $\Rightarrow$ JPred Secondary Structure
-Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear.
-Note that the number of sequences in the results window is many more than in the original alignment as
-JPred performs a PSI-BLAST search to expand the prediction dataset. The results
+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. The results
from the prediction are visible in the annotation panel. JPred secondary
-structure prediction annotations are examples of sequence-associated alignment annotation. }
+structure prediction annotations are examples of sequence-associated alignment annotation. {\sl Note:} The number of sequences in the results
+window is many more than in the original alignment as
+JPred performs a PSI-BLAST search to expand the prediction dataset.}
% TODO: check how long this takes - about 2 mins once it gets on the cluster.
\exstep{
Select a different sequence and perform a JPred prediction in the same way.
}
\exstep{
When you get the result, verify that the prediction has not been made for the
-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
+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}. The JPred reliability scores
differ from the prediction made on the full profile.
}
\exstep{
-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.
-
+In the original alignment that you loaded in step {\sl a}, select {\bf all}
+sequences ([CTRL]-A or [CMD]-A), then open the {\sl Sequence ID $\Rightarrow$ Selection $\Rightarrow$ Add
+Reference Annotation} submenu
+by right clicking the mouse to open the context menu.
{\bf All} the JPred predictions for the sequences will now be visible in the
original alignment window.}
-
-{\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
+ {\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
follow the instructions to view the Jalview annotations file created from the annotations
generated by the JPred server for your sequence.
\bf See the video at:
\textbf{REMARK465} ``Missing
coordinates in X-ray structure as defined by remark465 entries in PDB.
Nonassigned electron densities most often reflect intrinsic disorder,
-and have been used early on in disorder prediction.'' Features give
+and have been used early on in disorder prediction'' . Features give
range(s) of residues predicted as disordered, and annotation rows gives
raw value for each residue. Values over 0.1204 indicates disorder.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/disorderpred.pdf}
-\caption{{\bf Shading alignment by sequence disorder}. Alignment of Interleukin IV homologs coloured with Blosum62 with protein disorder prediction sequence features overlaid, shaded according to their score. Borderline disordered regions appear white, reliable predictions are either Green or Brown depending on the type of disorder prediction. }
+\caption{{\bf Shading alignment by sequence disorder}. Alignment of Interleukin IV homologs coloured with Blosum62 with protein
+disorder prediction sequence features overlaid, shaded according to their score. Borderline disordered regions appear white,
+reliable predictions are either Green or Brown depending on the type of disorder prediction. }
\label{alignmentdisorder}
\end{center}
\end{figure}
by default, but can be shown by right-clicking on the alignment
annotation panel and selecting \textbf{Show hidden annotation}.
-\exercise{Protein Disorder Prediction}{
+\exercise{Protein Disorder Prediction}
+{
\label{protdisorderex}
-{\sl Before starting this exercise, make sure you enable the \protect{`Add
-Temperature Factor'} option in your {\bf Structures} preferences. }
+{\sl Note:} Before starting this exercise, make sure you enable the \protect{{\sl Add
+Temperature Factor annotation to alignment}} option in your Structures preferences
+({\sl Tool $\Rightarrow$ Preferences $\Rightarrow$ Structure)}.
-\exstep{Open the alignment using
+\exstep{Open the alignment from
\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
\exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
-$\Rightarrow$ Disorder Prediction }.}
+$\Rightarrow$ Disorder Prediction $\Rightarrow$ Disembl with defaults}.}
-\exstep{Select all the sequences. Open the Structure Chooser by placing
+\exstep{Select all the sequences ([CTRL]-A or [CMD]-A). Open the Structure Chooser by placing
the mouse in the Sequence ID panel, right clicking the mouse and select
{\sl$\Rightarrow$ 3D Structure Data\ldots }. Select all structures in the list.
-Hit the View button to retrieve and show all PDB structures for the sequences.}
+Hit the {\sl New View} button to retrieve and show all PDB structures for the sequences.}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
\exstep{Features on sequences can conceal other colouring. This can be
toggled off by selecting {\sl View
-$\Rightarrow$ Show Sequence Features}.}
+$\Rightarrow$ Show Sequence Features} in the alignment window menu.}
\exstep{Apply the IUPred disorder prediction method. Tick the
-the {\sl Per sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog
+{\sl Per sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog
box. Then shade the sequences by the long and short disorder predictors. {\sl
-Note how well the disordered regions predicted by each method agree
-with the structure.}}
+Note} how well the disordered regions predicted by each method agree
+with the structure.}
\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
\chapter{Webservices}
+
+\section{What are Web Services ?}
+
\label{jvwebservices}
The term ``Webservices'' refers to a variety of data exchange
mechanisms based on HTTP.\footnote{HTTP: Hyper-Text Transfer Protocol.}
progress of running jobs.
-\subsection{JABA Web Services for Sequence Alignment and Analysis}
+\section{JABA Web Services for Sequence Alignment and Analysis}
\label{jabaservices}
JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
by Peter Troshin and Geoff Barton at the University of Dundee for running
git://source.jalview.org / jalview-manual.git / blobdiff