\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 1.2.2
-8th June 2010
+4th March 2011
\end{center}
\clearemptydoublepage
-% ($Revision$) 1st September 2008.}
+% ($Revision$) 11th October 2010.}
+% TODO revise for 2.6
\pagenumbering{roman}
\setcounter{page}{1}
\exstep{Open the Jalview Desktop's user preferences dialog (from the Tools
menu), and untick the checkbox adjacent to the 'Open file' entry in the
'Visual' preferences tab.}
-\exstep{Click OK to save the preferences, then close Jalview and launch it
-again. The example alignment should not be loaded when Jalview starts up.}
-}
-
+\exstep{Click OK to save the preferences, then \em{launch another Jalview
+instance from the web site}. The example alignment should not be
+loaded when the new Jalview instance starts up.}
+{\sl Note: Should you want to reload the example alignment, then select the
+{\em File$\Rightarrow$ From URL} entry from the Desktop menu, and click on the
+URL history button on the right hand side of the dialog box that opens to
+recover the example file's URL, followed by OK, to open the file. } }
\subsection{Getting Help}
\label{gettinghelp}
\exstep{
Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the {\sl PFAM (seed)} database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load.
}
-\exstep{Open the URL \textsf{http://www.jalview.org/tutorial/alignment.fa} in a web browser. Select and copy the entire text to the clipboard (usually via the browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} . Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$ Paste} text box menu option. Click {\sl Close} and the alignment will be loaded.
-}
-}
+\exstep{Open the URL \textsf{http://www.jalview.org/tutorial/alignment.fa} in a
+web browser. Select and copy the entire text to the clipboard (usually via the
+browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running
+and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} .
+Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
+Paste} text box menu option. Click {\sl New Window} and the alignment will be
+loaded. } }
\subsection{Memory Limits}
\label{memorylimits}
\exercise{Saving Alignments}{
\label{save}
-\exstep{Start Jalview, close all windows and load the ferrodoxin alignment from pFam (accession number PF03460 (see Exercise \ref{load}).
+\exstep{Start Jalview, close all windows and load the ferredoxin alignment from pFam (accession number PF03460 (see Exercise \ref{load}).
}
\exstep{
Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a location into which to save the alignment and select a format. All formats except {\sl Jalview } can be viewed in a normal text editor (e.g. Notepad) or in a web browser. Enter a file name and click {\sl Save}. Check this file by browsing to it with your web browser or by closing all windows and opening it with Jalview.
\exstep{ Repeat the previous step trying different file formats.}
\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}. You can select and copy this alignment to the clipboard using the textbox menu options {\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}. The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
}
-\exstep{Ensure at least one alignment window is shown in Jalview. Open the overview window and scroll to any part of the alignment. Select {\sl File $\Rightarrow$ Save Project} from the main menu and save in a suitable place. Close all windows and then load the project via the {\sl File $\Rightarrow$ Save Project} menu option. Note how all the windows and positions are exactly as they were when they were saved.
-}
-}
+\exstep{Ensure at least one alignment window is shown in Jalview. Open the
+overview window and scroll to any part of the alignment. Select {\sl File
+$\Rightarrow$ Save Project} from the main menu and save in a suitable place.
+Close all windows and then load the project via the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } }
\r\r\section{Selecting and editing sequences}
\label{selectingandediting} \rJalview makes extensive use of selections - most of the commands available from
its menus operate on the currently selected region of the alignment, either to
\r\subsection{Selecting parts of an alignment}
Selections can be of arbitrary regions in an alignment, one or more complete columns, or one or more complete sequences.
-A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ As New Alignment} alignment window menu options.
+A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ New Alignment} alignment window menu options.
To clear (unselect) the selection press the [ESC] (escape) key.
\subsubsection{Making selections in Cursor mode}
-To define a selection in cursor mode, navigate to the top left corner of the proposed selection. Pressing the [Q] key marks this as the corner. A red outline appears around the cursor (Figure \ref{cselect})
+To define a selection in cursor mode (which is enabled by pressing [F2]),
+navigate to the top left corner of the proposed selection (using keystroke
+commands, the arrow keys or the mouse). Pressing the [Q] key marks this as the
+corner. A red outline appears around the cursor (Figure \ref{cselect})
Navigate to the bottom right corner of the proposed selection and press the [M] key. This marks the bottom right corner of the selection. The selection can then be treated in the same way as if it had been created in normal mode.
visible, and then invert the selection.\footnote{It is also possible to hide
everything but the selected region using the {\sl View $\Rightarrow$ Hide
$\Rightarrow$ All but selected region } menu entry.}
-\r\r\subsection{Creating groups}\rSelections are lost as soon as a different region is selected. Groups can be 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 $\Rightarrow$ Group} then enter a name for the group in the dialogue box which appears.
+\r\r\subsection{Creating groups}\rSelections are lost as soon as a different region is selected. Groups can be
+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 Group Name}\footnote{In earlier versions
+of Jalview, this entry was variously 'Group' or 'JGroupXXXXX' (Where XXXXX was
+some serial number).} then enter a name for the group in the dialogue box which
+appears.
\begin{figure}
\begin{center}
\exercise{Making selections and groups}{
\label{exselect}
-\exstep{Close all windows in Jalview and load the ferrodoxin alignment (PFAM ID PF03460). Choose a residue and place the mouse cursor on it. Click and drag the mouse cursor to create a selection. As you drag, a red box will `rubber band' out to show the extent of the selection. Release the mouse button and a red box should border the selected region. Now press [ESC] to clear the selection.}
-\exstep{
+\exstep{Close all windows in Jalview and load the ferredoxin alignment (PFAM
+ID PF03460). Choose a residue and place the mouse cursor on it. Click and drag the mouse cursor to create a selection. As you drag, a red box will `rubber band' out to show the extent of the selection. Release the mouse button and a red box should border the selected region. Now press [ESC] to clear the selection.} \exstep{
Select one sequence by clicking on the id panel. Note that the sequence ID takes on a highlighted background and a red box appears around the selected sequence. Now 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.
Now hold down [CTRL] and click on several sequences ID's both selected and unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are individually deselected.
}
\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
\exercise{Editing alignments}{
\label{mousealedit}
+% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
+
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
-ferrodoxin alignment from PF03460.
+ferredoxin alignment from PF03460.
You are going to manually reconstruct the alignment that jalview loads by
- default. Remember to use [CTRL]+Z to undo an edit, or the {\tr File $\LeftArrow$
- Reload } function to revert the alignment back to the original version if you
- want to start again.
+ default. Remember to use [CTRL]+Z to undo an edit, or the {\tr File
+ $\Rightarrow$ Reload } function to revert the alignment back to the original
+ version if you want to start again.
}
\exstep{ Select the first 7 sequences, and press H to hide them (or right click
dragging one column to right. Insert another gap at column 47 in all sequences in
the same way.}
-\exstep{ Correct the feredoxin domain alignment for FER1\_SPIOL by
+\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
insert two additional gaps after the gap at column 47: hold [SHIFT] and click and
drag on the G and move it two columns to the right.}
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).
\exstep{Load the sequence alignment at \textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the edited alignment from exercise \ref{mousealedit}. If you continue from the previous exercise, then first right click on the sequence ID panel and select {\tr Reveal All}.
Now, enter cursor mode by pressing [F2]}
+%TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
\exstep{Insert 58 gaps at the start of the first sequence (FER\_CAPAA). Press {\sl 58} then {\sl [SPACE]}. }
\exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN). Hold down shift and click on the fifth (FER1\_PEA). }
\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing {\sl 1,2} then pressing {\sl [RETURN]}. Now insert 6 gaps. Type {\sl 6} then hold down [CTRL] and press the space bar.}
\end{figure}
\subsection{Shading by conservation}
-For many colour schemes, the intensity of the colour in a column can be scaled by the degree of amino acid property conservation. Selecting {\sl Colour $\Rightarrow$ By Conservation} brings up a selection box (the {\sl Conservation Threshold dialog box}) allowing the alignment colouring to be modified. Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}).
+For many colour schemes, the intensity of the colour in a column can be scaled
+by the degree of amino acid property conservation. Selecting {\sl Colour
+$\Rightarrow$ By Conservation} enables this mode, and {\sl Modify
+conservation threshold} brings up a selection box (the {\sl Conservation
+Threshold dialog box}) allowing the alignment colouring to be modified.
+Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}).
\begin{figure}[htbp]
\begin{center}
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.
}
Jalview can calculate and display trees, providing interactive tree-based grouping of sequences though a tree viewer. All trees are calculated via the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu. Trees can be calculated from distance matrices determined from \% identity or aggregate BLOSUM 62 score using either average distance (UPGMA) or Neighbour joining algorithms. The input data for a tree calculation is either the visible portions of the current selection, or the whole alignment if no selection is present.
On calculating a tree, a new window opens (Figure \ref{trees1}) which contains
-the tree. Various display options can be found in the tree window {\sl View}
-menu, and export options in the {\sl File $\Rightarrow$ Save As} submenu.
-Newick format is a standard file format for trees which allows them to be
-exported to other programs. Jalview can also read in external trees in Newick
-format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf
-names on imported trees will be matched to the associated alignment - unmatched
+the tree. Various display settings can be found in the tree window {\sl View}
+menu, including font, scaling and label display options, and the {\sl File
+$\Rightarrow$ Save As} submenu contains options for image and Newick file
+export. Newick format is a standard file format for trees which allows them to
+be exported to other programs. Jalview can also read in external trees in Newick format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf names on imported trees will be matched to the associated alignment - unmatched
leaves will still be displayed, and can be highlighted using the {\sl View
$\Rightarrow$ Show Unlinked Leaves} menu option.
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 / blobdiff