\vspace{2in}
Manual Version 1.9
-% for CLS lifesci course 2017 & St Andrews course
-% Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-20th February 2017
+
+Manual Version 1.8.1
+% post CLS lifesci course on 15th January
+% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
+
+10th November 2017
+
+
\end{center}
\section{Introduction}
\subsection{Jalview}
Jalview is a multiple sequence alignment viewer, editor and analysis tool.
-Jalview is designed to be platform independent (running on Mac, MS Windows, Linux
+It is designed to be platform independent (running on Mac, MS Windows, Linux
and any other platforms that support Java). Jalview is capable of editing and
analysing large alignments (thousands of sequences) with minimal degradation in
-performance, and able to show multiple integrated views of the alignment and
-other data. Jalview can read and write many common sequence formats including
+performance. It is able to show multiple integrated views of the alignment
+and other data. Jalview can read and write many common sequence formats including
FASTA, Clustal, MSF(GCG) and PIR.
alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
-The Jalview Desktop in this version
-provides access to protein and nucleic acid sequence, alignment and structure
+The Jalview Desktop provides access to protein and nucleic acid sequence, alignment and structure
databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
-\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of
-RNA secondary structure. It also
+\url{http://www.jmol.org}} and Chimera viewer for molecular structures, and the
+VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. It also
provides a graphical user interface for the multiple sequence alignment, conservation analysis
and protein disorder prediction methods provided as {\bf Ja}va {\bf B}ioinformatics
{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS). JABAWS\footnote{released under GPL at \url{http://www.compbio.dundee.ac.uk/jabaws}} is a system for
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 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.
+Section \ref{featannot} details the creation and visualization of sequence,
+features and alignment annotation. Section \ref{workingwithnuc} discusses
+specific features of use when working with nucleic acid sequences, such as translation and linking to protein coding regions, and the display and analysis of RNA secondary structure.
%^Chapter \ref{jalviewadvanced} The third chapter covers the detail^ of Jalview and is aimed at the user who is
%already familiar with Jalview operation but wants to get more out of their
This tutorial is based on the Jalview
Desktop application. Much of the information will also be useful for users of
-the JalviewLite applet, which has the same core editing, analysis and visualization capabilities (see the
-\href{http://www.jalview.org/examples/applets.html}{JalviewLite Applet Examples}
-page for examples). The Jalview Desktop, however, is much more powerful, and
+the JalviewLite applet, which has the same core editing, analysis and visualization capabilities. The Jalview Desktop, however, is much more powerful, and
includes additional support for interaction with external web services, and
production of publication quality graphics.
the application starts. If your browser is not set up to handle webstart, then
clicking the launch link may download a file that needs to be opened
manually, or prompt you to select the program to handle the webstart
-file. If that is the case, then you will need to locate the {\bf javaws} program
+file. If that is the case, you will need to locate the {\bf javaws} program
on your system\footnote{The file that is downloaded will have a type of {\bf
application/x-java-jnlp-file} or {\bf .jnlp}. The {\bf javaws} program that can run
this file is usually found in the {\bf bin} directory of your Java
\label{gettinghelp}
\subsubsection{Built in Documentation}
Jalview has comprehensive on-line help documentation. Select {\sl Help
-$\Rightarrow$ Documentation} from the main window menu and a new window will
-open (Figure \ref{help}). The appropriate topic can then be selected from the
+$\Rightarrow$ Documentation} from the main desktop window menu and a new window
+will open (Figure \ref{help}). The appropriate topic can then be selected from the
navigation panel on the left hand side. To search for a specific topic, click
the `search' tab and enter keywords in the box which appears.
%Jalview provides many ways to load your own sequences. %For this section of the
% tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
\subsection{Drag and Drop}
- In most operating systems you can just drag a file icon from a file browser
+ In most operating systems you can drag a file icon from a file browser
window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended.
Drag and drop also works when loading data from a URL -
-simply drag the link or url from the address panel of your browser on to an
+simply drag the link or url from the address panel of your browser onto an
alignment or the Jalview desktop background and Jalview will load data from the
URL directly.
% (Figure \ref{drag})
A selected region can be copied and pasted as a new alignment
using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ To New
Alignment} in the alignment window menu options.
-{\bf To clear (unselect) the selection press the [ESC] (escape) key.}
+{\bf To clear (unselect) the selection press the [ESC] key.}
\subsection{Selecting Arbitrary Regions}
To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button.
Discontinuous regions can be selected by holding down [CTRL] and clicking on
positions to add to the column selection. Note that each [CTRL]-Click (PC) or
[CMD]-Click (Mac) changes the current selected sequence region to that column,
-but adds to the column selection.
+it adds to the column selection.
Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
%[fig 13]
To select multiple complete sequences, click and drag the mouse down the
sequence ID panel. The same techniques as used for columns (above) can be used
-with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous
+with [SHIFT]-Click for continuous and [CTRL]-Click (or
+[CMD]-Click for Mac) to select discontinuous
ranges of sequences (Figure \ref{selectrows}).
%[fig 14]
\subsection{Representing a Group with a Single Sequence}
-Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
+Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence.
+The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant
+of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other.
+Note, any alignment edits that affect the sequence will also affect the whole
+sequence group.
\exercise{Hiding and Revealing Regions}{
\exstep{Close windows.
\subsection{Multiple Alignment Views}
-Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\sl Views}. Because each view displays the same underlying data, any edits performed in one view will update the alignment or annotation visible in all views.
+Jalview is able to create multiple independent visualizations of the same underlying alignment - these are called {\sl Views}.
+Because each view displays the same underlying data, any edits performed in one view will update the alignment or annotation visible in all views.
-\parbox[c]{4in}{Alignment views are created using the {\sl View $\Rightarrow$ New View} option of the alignment window or by Pressing [CTRL]-T. This will create a new view with the same groups, alignment layout and display options as the current one. Pressing G will gather together Views as named tabs on the alignment window, and pressing X will expand gathered Views so they can be viewed simultaneously in their own separate windows. To delete a group, press [CTRL]-W.}\parbox[c]{2.75in}{
+\parbox[c]{4in}{Alignment views are created using the {\sl View $\Rightarrow$
+New View} option of the alignment window or by pressing [CTRL]-T.
+This will create a new view with the same groups, alignment layout and display options as the current one.
+Pressing G will gather together Views as named tabs on the alignment window, and pressing X will expand gathered Views so they can be viewed
+simultaneously in their own separate windows. To delete a group, press [CTRL]-W.}\parbox[c]{2.75in}{
\begin{center}\centerline{
\includegraphics[width=2.5in]{images/mulv_tabs.pdf}}
\end{center}
% move to ch. 3 ?
%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
-\subsubsection{Recovering input Data for a Tree or PCA Plot Calculation}
+\subsubsection{Recovering input data for a Tree or PCA Plot Calculation}
\parbox[c]{5in}{
The {\sl File $\Rightarrow$ Input Data } option will open a new alignment window containing the original data used to calculate the tree or PCA plot (if available). This function is useful when a tree has been created and then the alignment subsequently changed.
}
\parbox[c]{1.25in}{\centerline{\includegraphics[width=1.25in]{images/pca_fmenu.pdf}
}}
-\subsubsection{Changing the associated View for a Tree or PCA Viewer}
+\subsubsection{Changing the associated view for a Tree or PCA Viewer}
\parbox[c]{4in}{
The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display according to the colouring and selection state of the newly associated view.
} \parbox[c]{3in}{\centerline{
\url{http://www.jalview.org/training/Training-Videos}.}
}
-\exercise{Tree Based Conservation Analysis}{
-\label{consanalyexerc}
-\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher.
-Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}, set {\sl Conservation} shading threshold at around 20. }
-\exstep{Build a Neighbour joining tree using Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using BLOSUM62}.}
-\exstep{Use the mouse cursor to select a point on the tree to partition the
-alignment into several sections.}
-\exstep {Select {\sl View $\Rightarrow$ Sort Alignment By Tree} option in the
-tree window to re-order the sequences in the alignment using the calculated
-tree.
-Examine the variation in colouring between different groups of sequences in the alignment
-window. }
-\exstep {You may find it easier to browse the alignment if you first uncheck the
-{\sl Annotations $\Rightarrow$ Show Annotations} option. Open the
-Overview Window within the View menu to aid navigation.}
-
-\exstep{Try changing the colourscheme of the residues in the alignment to
-BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected).}
-{\sl Note: You may want to save the alignment and tree as a project file, since
-it is used in the next set of exercises. }
-
-{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
-}
+% \exercise{Tree Based Conservation Analysis}{
+%\label{consanalyexerc}
+%\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher.
+%Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}, set
+% {\sl Conservation} shading threshold at around 20. } \exstep{Build a Neighbour joining tree using Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
+%Neighbour Joining Using BLOSUM62}.}
+%\exstep{Use the mouse cursor to select a point on the tree to partition the
+%alignment into several sections.}
+%\exstep {Select {\sl View $\Rightarrow$ Sort Alignment By Tree} option in the
+%tree window to re-order the sequences in the alignment using the calculated
+%tree.
+%Examine the variation in colouring between different groups of sequences in the
+% alignment window. }
+%\exstep {You may find it easier to browse the alignment if you first uncheck
+% the {\sl Annotations $\Rightarrow$ Show Annotations} option. Open the
+%Overview Window within the View menu to aid navigation.}
+
+%\exstep{Try changing the colourscheme of the residues in the alignment to
+%BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected).}
+%{\sl Note: You may want to save the alignment and tree as a project file, since
+%it is used in the next set of exercises. }
+
+%{\bf See the video at:
+%\url{http://www.jalview.org/training/Training-Videos}.}
+%}
\subsection{Redundancy Removal}
Note that the {\sl Select many views} option is useful if you have different
views that colour different areas or domains of the alignment. This option is
-further explored in Section \ref{complexstructurecolours}.
+further explored in exercise \ref{complexstructurecolours}.
\exercise{Aligning Structures using the Ferredoxin
git://source.jalview.org / jalview-manual.git / blobdiff