\title{Jalview 2.5: A manual and introductory tutorial }
\author{David Martin, James Procter, Andrew Waterhouse and Geoff Barton}
-\date{Manual version 1.2 9st June 2010}
+\date{Manual version 1.2.1 11th October 2010}
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}}\cleardoublepage}
\vspace{2in}
-Manual version 1.2
+Manual version 1.2.1
-8th June 2010
+11th October 2010
\end{center}
\clearemptydoublepage
-% ($Revision$) 1st September 2008.}
+% ($Revision$) 11th October 2010.}
+% TODO revise for 2.6
\pagenumbering{roman}
\setcounter{page}{1}
\subsubsection{Undoing edits}
Jalview supports the undoing of edits via the {\sl Edit $\Rightarrow$ Undo Edit} alignment window menu option. Each editing action is stored and can be reversed in sequence. Colouring of the alignment is not reversible via the {\sl Undo} option.
-\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 with [SHIFT] pressed.}
-\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}
% % better idea to introduce hiding sequences, and use the invert selection, hide
% others, to simplify manual alignment construction
edits you have made}
}
+\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 with [SHIFT] pressed.}
+\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}
+
+
\subsubsection{Editing in Cursor mode}
Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by pressing [SPACE]. Gaps will be inserted at the cursor, pushing 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).
Jalview can automatically determine which structures are associated with a
sequence if that sequence has an ID from a public database that contains
cross-references to the PDB, such as Uniprot. Right-click on any sequence ID and
-select {\sl $<$Sequence ID$>$ $\Rightarrow$ Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the
-context menu (where {\sl $<$Sequence ID$>$} is the ID of the sequence on which
+select {\sl $<$Sequence ID$>$ $\Rightarrow$ Structure $\Rightarrow$
+Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (where {\sl $<$Sequence ID$>$} is the ID of the sequence on which
you clicked) (Figure \ref{auto}). Jalview will attempt to associate the
sequence with a Uniprot sequence and from there discover any associated PDB
structures. This takes a few seconds and applies to all sequences in the
\subsection{Viewing Protein Structures}
The structure viewer can be launched through the sequence ID context menu.
-Select {\sl Structure $\Rightarrow$ View PDB entry $\Rightarrow$ $<$PDB
+Select {\sl Structure $\Rightarrow$ View Structure $\Rightarrow$ $<$PDB
ID$>$}. The structure 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
\exercise{Viewing Structures}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Associate Structure with Sequence $\Rightarrow$ Discover PDB ids}. Jalview will now attempt to find PDB structures for the sequences in the alignment.
-}
-\exstep{
-Right-click on the sequence ID for {\sl FER1\_SPIOL}. Select { \sl FER1\_SPIOL $\Rightarrow$ View PDB Entry: 1A70} A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel.
-}
-\exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence.
-}
-\exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press {\sl OK} to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with your web browser.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the
+sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up
+the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
+Associate Structure with Sequence $\Rightarrow$ Discover
+PDB ids}. Jalview will now attempt to find PDB structures for the sequences in
+the alignment. } \exstep{ Right-click on the sequence ID for {\sl FER1\_SPIOL}.
+Select { \sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$ View Structure
+$\Rightarrow$ 1A70} A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel. } \exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. } \exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press {\sl OK} to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with your web browser. }
\exstep{Select {\sl File $\Rightarrow$ View Mapping} from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.}
\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file. Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$ Show Labels} menu option, and the plot background colour changed 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 via the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
\exercise{Principle Component Analysis}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/examples/exampleFile.jar} and select {\sl Edit $\Rightarrow$ Undefine Groups}.
-}
-\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/examples/exampleFile.jar} and select {\sl Select
+$\Rightarrow$ Undefine Groups}. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
\exstep{
Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups, each of a different colour. Note how the colour of the sequence ID label matches both the colour of the partitioned tree and the points in the PCA plot.
}
can help when working with larger alignments.
\exercise{Tree Based Conservation Analysis}{
+\label{consanalyexerc}
\exstep{Load the PF03460 Seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the sort submenu to order alignment using the calculated tree.}
\exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
\end{figure}
\exercise{Remove redundant sequences}{
-\exstep{Re-use or recreate the alignment and tree which you worked with in the tree based conservation analysis exercise (exercise \ref{treeconsanaly})}
+\exstep{Re-use or recreate the alignment and tree which you worked with in the
+tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% similar under this alignment.}
\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Show Linked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
\exstep{Use the [Undo] button on the dialog to recover the sequences. Note that the * symbols disappear from the tree display.}
Visual tab in the Jalview desktop's preferences dialog box.
\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{treeconsanaly})}
-\exstep{Create a new view, and ensure the annotation panel is displayed, and
+\exstep{Re-use or recreate the alignment and tree which you worked with in the
+tree based conservation analysis exercise (exercise \ref{consanalyexerc})} \exstep{Create a new view, and ensure the annotation panel is displayed, and
enable the display of {\sl Group Consensus}, and the display of sequence
logos to make it easier to see the different residue populations within each group.}
\exstep{Select a column exhibiting about 50\% conservation that lies within the
git://source.jalview.org / jalview-manual.git / commitdiff