\vspace{0.5in}
{\huge
-Manual with Introductory Tutorial }
+Manual and Introductory Tutorial }
\vspace{2.4in}
\vspace{2in}
-Manual Version 1.5
+Manual Version 1.5.1
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-4th December 2014
+24th April 2015
\end{center}
\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
-and any other platforms that supports Java). Jalview is capable of editing and
+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
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
-{\bf Pfam}.\footnote{\url{http://pfam.sanger.ac.uk}}
+colouring.} and includes a javascript API to allow customisable display of
+alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
visualization of sequence alignments, and their interactive analysis. Tree
building, principal components analysis, physico-chemical property conservation
and sequence consensus analyses are built into the program. Web services enable
-Jalview to access on line alignment and secondary structure prediction programs,
+Jalview to access online alignment and secondary structure prediction programs,
as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
\begin{figure}[htbp]
\begin{center}
between Jalview, TOPALi and AstexViewer.} in 2004, enabling Andrew Waterhouse and
Jim Procter to re-engineer the original program to introduce contemporary developments
in bioinformatics and take advantage of the latest web and Java technology.
-Jalview's development was supported from 2009
-by an award from the BBSRC's Tools and Resources fund. Jalview's development is
-currently being funded by a BBSRC `Extending The Jalview Resource for
-Biological Sequence Alignment and Analysis' grant and a Wellcome Trust
-`Extending The Jalview Resource for Biological Sequence Alignment and Analysis'
-grant. In 2010, 2011, and 2012, Jalview benefitted from the
+Jalview's development has been supported from 2009
+by awards from the BBSRC's Tools and Resources fund, and, since 2014, a Wellcome Trust Biomedical Resource grant\footnote{Wellcome grant number 101651/Z/13/Z}. In 2010, 2011, and 2012, Jalview benefitted from the
\href{http://code.google.com/soc/}{Google Summer of Code}, when Lauren Lui and Jan Engelhardt introduced new features for handling RNA alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
(Figure \ref{download}).
These links will launch the latest stable release of Jalview.\par
+%% 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
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
\end{figure}
-\exercise{Launching Jalview from the Jalview website}{
+\exercise{Launching Jalview from the Jalview Website}{
\label{start}
\exstep{Open the Jalview web
site \href{http://www.jalview.org}{(www.jalview.org)}
\exstep{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
the URL history button on the right hand side of the dialog box to view the
-files, selected exampleFile-2-7.jar, then click OK.}
+files, select exampleFile\_2\_7.jar, then click OK.}
{\bf Note:} Should you want to reload the example alignment or load your own
sequence during the launch process, then go
to the {\sl Tools $\Rightarrow$
\subsection{Getting Help}
\label{gettinghelp}
-\subsubsection{Built in documentation}
+\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
\end{center}
\end{figure}
-\subsubsection{Email lists}
+\subsubsection{Email Lists}
The Jalview Discussion list {\tt jalview-discuss@jalview.org} provides a forum
for Jalview users and developers to raise problems and exchange ideas - any
Rapid movement to specific positions is accomplished as listed below:
\begin{list}{$\circ$}{}
-\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to move to sequence (row) {\sl n}
+\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to
+move to sequence (row). {\sl n}
\item {\bf Jump to Column {\sl n}:} Type a number {\sl n} then press [C] to move to column {\sl n} in the alignment.
\item {\bf Jump to Residue {\sl n}:} Type a number {\sl n} then press [P] to move to residue number {\sl n} in the current sequence.
\item {\bf Jump to column {\sl m} row {\sl n}:} Type the column number {\sl m}, a comma, the row number {\sl n} and press [RETURN].
\exstep{Find the Overview Window, {\sl Views
$\Rightarrow$ Overview Window} and open it. Move around the
alignment by clicking and dragging the red box in the overview window.}
-\exstep{Look at the status bar (lower left hand corner of the alignment window) as
-you move the mouse over the alignment. It indicates information about the
+\exstep{Return to the alignment window. Look at the status bar (lower left hand
+corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
sequence and residue under the cursor.}
-\exstep{Press [F2] to enter {\bf Cursor mode}. Use the direction {\bfarrow
-keys} to move the cursor around the alignment.}
+\exstep{Press [F2] key (or [Fn]/[F2] on Mac) to enter {\bf Cursor mode}. Use
+the direction {\bfarrow keys} to move the cursor around the alignment.}
\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
two different positions if gaps are inserted into the sequence. Move to sequence 5,
\end{figure}
-\exercise{Loading sequences}{
+\exercise{Loading Sequences}{
\label{load}
\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
close all windows.}
sources.
Select the {\bf PFAM seed} database and click ok, then enter the accession
-number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
+number {\bf PF03460} and click OK. An alignment of about 174 sequences should
+load, these can be viewed using the Overview window accessible from {\sl View
+$\Rightarrow$ Overview Window.}.
Several database IDs
or accession numbers can be loaded by using semicolons to separate them.}}
To define a selection in cursor mode (which is enabled by pressing [F2] when the alignment window is selected),
navigate to the top left corner of the proposed selection (using the mouse, the arrow keys, or the keystroke
commands described in Section \ref{cursormode}). Pressing the [Q] key marks this as the
-corner. A red outline appears around the cursor (Figure \ref{cselect})
+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.
This may also be useful when hiding large regions in an alignment (see Section \ref{hidingregions} below).
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
-$\Rightarrow$ Selected Region }.
+$\Rightarrow$ Selected Region}.
\subsection{Creating Groups}
Selections are lost as soon as a different region is selected. Groups can be
This will turn the selected region into a group and colour it accordingly.}
\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
-to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
+to include newly selected sequences, and the `Percentage Identity' colouring changes. }
+\exstep{ Another way to resize the group is by using the mouse to click and drag
+the right-hand edge of the selected group.}
\exstep{The current selection can be {\bf exported} and saved by right clicking
on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
-\exercise{Hiding and revealing regions}{
+\exercise{Hiding and Revealing Regions}{
\exstep{Close all windows, open the PFAM accession PF03460. Select a
contiguous set of sequences by clicking and dragging on the sequence ID panel.
Right click on the selected sequence IDs to bring up the sequence ID pop-up
Sequence ID and in the pop-up menu select Reveal All.}}
+\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}
+
+
\subsection{Introducing and Removing Gaps}
\subsubsection{Introducing Gaps in a Single Sequence}
-To introduce a gap, 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.
+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.
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.
\subsubsection{Introducing Gaps in all Sequences of a Group}
-To insert gaps in all sequences in a selection or group, 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.
+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.
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).
\subsubsection{Sliding Sequences}
Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the selected sequences to the left or
-right (respectively). Slides occur regardless of the region selection -
+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.
Sequences}). }
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
-the left so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
+the right so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
O80429\_MAIZE
}
-\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}
-
-
\subsubsection{Editing in Cursor mode}
Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
\ref{mousealedit}, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
-{\bf {\sl Note for Windows Users:}} The [SHIFT]-[SPACE] command has the same effect as
-the [CTRL]-[SPACE] command mentioned in this exercise, and you should use
-[SHIFT]-[SPACE] in order to avoid opening the window menu.}
+{{\bf Note:}} For Mac users, [CTRL]-[SPACE] command
+has the same effect as the [SHIFT]-[SPACE] command mentioned in this exercise.
+
+Window users should use [SHIFT]-[SPACE] rather than the [CTRL]-[SPACE] command,
+as this command will close the window.}
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
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{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 press {\sl [RETURN]}. Now insert 6 gaps in all the sequences.
-Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.} \exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
-Press {\sl 34C} then {\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE].
-Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are
-now aligned.}
+Type {\sl 6} then hold down {\sl [SHIFT]} and press {\sl [SPACE]}.}
+\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
+Press {\sl 34C} then {\sl [SHIFT]-[SPACE]}. Press {\sl 38C} then
+[SHIFT]-[SPACE].
+Press {\sl 47C} then {\sl 3 [SHIFT-SPACE]} the first through fourth sequences
+are now aligned.}
\exstep{The fifth sequence (FER1\_PEA) is poorly aligned. We will delete some gaps and add some new ones. Press {\sl [ESC]} to clear the selection. Navigate to the start of sequence 5 and delete 3 gaps. Press {\sl 1,5 [RETURN]} then {\sl 3 [BACKSPACE]} to delete three gaps. Go to column 31 and delete the gap. Press {\sl 31C [BACKSPACE]} .}
\exstep{ Similarly delete the gap now at column 34, then insert two gaps at column 38. Press {\sl 34C [BACKSPACE] 38C 2 [SPACE]}. Delete three gaps at column 44 and insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are now aligned.}
}
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Features} option before you can see your colourscheme.
-There are two main types of colouring styles: {\bfsimple static residue}
-colourschemes and {\bfdynamic schemes} which use conservation and consensus
-analysis to control colouring. A {\bfhybrid colouring} is also possible, where
+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.
\subsection{Colouring the Whole Alignment}
}\parbox[c]{3in}{
\centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
-The {\bf per Sequenc only} option in the {\bf Colour By Annotation} dialog
+The {\bf per Sequence} option in the {\bf Colour By Annotation} dialog
allows each sequence to be shaded according to sequence associated annotation
rows, such as protein disorder scores. This functionality is described further
in Section \ref{protdisorderpred}.
\subsubsection{Taylor}
\parbox[c]{3.5in}{
-This colour scheme was devised by Willie Taylor and an entertaining description of it's origin can be found in Protein Engineering, Vol 10 , 743-746 (1997)
+This colour scheme was devised by Willie Taylor and an entertaining description of its origin can be found in Protein Engineering,
+Vol 10 , 743-746 (1997).
}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_taylor.pdf}
\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
-sequences and alignments, see Section \ref{workingwithnuc}
+sequences and alignments, see Section \ref{workingwithnuc}.
%and Section \ref{workingwithrna}
-.
} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_purpyr.pdf} }
-\subsubsection{RNA Helix colouring}
+\subsubsection{RNA Helix Colouring}
\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
Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
}
\exstep{
-Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in exercise \ref{exselectgrpcolour} during the group selection step).
+Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group
+of around 4 similar sequences. Use the context menu (right click on the group)
+option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
+$\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which
+were not coloured are now coloured. The calculations performed for dynamic
+colouring schemes like Blosum62 are based on the group being coloured, not the
+whole alignment (this also explains the colouring changes observed in exercise
+\ref{exselect} during the group selection step).
}
\exstep{
-Keeping the same selection as before, colour the complete alignment using {\sl Colour $\Rightarrow$ Taylor}. Select the menu option {\sl Colour $\Rightarrow$ By Conservation}. Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
+Keeping the same selection as before, colour the complete alignment except
+the group using {\sl Colour $\Rightarrow$ Taylor}.
+Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
+Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
}
}
\end{figure}
-\exercise{User defined colour schemes}{
+\exercise{User Defined Colour Schemes}{
\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.
}
\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.
Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
sequence ID format and so on. }
-\exstep{Hide all the annotation rows by selecting {\sl View $\Rightarrow$ 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
+\exstep{Hide all the annotation rows by selecting {\sl Annotations $\Rightarrow$
+Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} \exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
annotation row labels to bring up the pop-up context menu, then select {\sl
Hide This Row}. Bring up the pop-up context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
available to Jalview users, and Section \ref{jabaservices} explains how to
configure the Jalview Desktop for access to new JABAWS servers.
Section \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS' AACon
+programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS AACon
service for protein multiple alignment conservation analysis.
Section \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS' protein disorder prediction
+structure predictions with JPred, and JABAWS protein disorder prediction
services are introduced in Section \ref{protdisorderpred}.
Section \ref{featannot} describes the mechanisms provided by Jalview for
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
-\section{Working with structures}
+\section{Working with Structures}
\label{wkwithstructure}
Jalview facilitates the use of protein structures for the analysis of alignments
by providing a linked view of structures associated with sequences in
the European Protein Databank (PDBe) using the Sequence Fetcher (see
\ref{fetchseq}).
-\subsection{Automatic association of PDB structures with sequences}
+\subsection{Automatic Association of PDB Structures with Sequences}
Jalview can automatically determine which structures are associated with a
sequence in a number of ways.
-\subsubsection{Discovery of PDB IDs from sequence database cross-references}
+\subsubsection{Discovery of PDB IDs from Sequence Database Cross-references}
If a 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 Structure $\Rightarrow$
Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (Figure \ref{auto}). Jalview will attempt to associate the
}
}
-\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence. After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and any associated PDB structures (right)}
+\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence.
+After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and
+any associated PDB structures (right).}
\label{auto}
\end{center}
\end{figure}
-\subsubsection{Drag-and-drop association of PDB files with sequences by filename
-match}
+\subsubsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
+Match}
\label{multipdbfileassoc}
If one or more PDB files stored on your computer are dragged from their location
on the file browser onto an alignment window, Jalview will search the alignment
If no associations are made, then sequences extracted
from the structure will be simply added to the alignment. However, if only
-some of the PDB files are associated, jalview will raise another dialog box giving
-you the option to add any remaining sequences from the PDB structure files not present in
+some of the PDB files are associated, Jalview will raise another dialog box
+giving you the option to add any remaining sequences from the PDB structure files not present in
the alignment. This allows you to easily decorate sequences in a newly imported
alignment with any corresponding structures you've already collected in a directory
accessible from your computer.\footnote{We plan to extend this facility in
\subsection{Viewing Structures}
+\label{viewAllStructures}
The structure viewer can be launched in two ways from the sequence ID context
menu. To view a particular structure associated with a sequence in the
alignment, simply select it from popup menu's associated structures submenu in
\end{center}
\end{figure}
-\subsection{Customising structure display}
+\subsection{Customising Structure Display}
Structure display can be modified using the {\sl Colour} and {\sl View} menus
in the structure viewer. The background colour can be modified by selecting the
sequence (How well and which parts of the structure relate to the sequence) can
be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
-\subsubsection{Using the Jmol visualization interface }
+\subsubsection{Using the Jmol Visualization Interface }
Jmol has a comprehensive set of selection and visualization functions that are
accessed from the Jmol popup menu (by right-clicking in the Jmol window or by
Verify that the Jmol display is as it was when you just saved the file.}
}
-\subsection{Superimposing structures}
+\subsection{Superimposing Structures}
\label{superposestructs}
Many comparative biomolecular analysis investigations aim to determine if the
biochemical properties of a given molecule are significantly different to its
$>$ 1) if the current selection contains two or more sequences with associated
structures.
-\subsubsection{Obtaining the RMSD for a superposition}
+\subsubsection{Obtaining the RMSD for a Superposition}
The RMSD (Root Mean Square Deviation) is a measure of how similar the structures
are when they are superimposed. Figure \ref{mstrucsuperposition} shows a
superposition created during the course of Exercise \ref{superpositionex}. The
$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
includes the precise atom pairs used to superpose structures.
-\subsubsection{Choosing which part of the alignment is used for structural
-superposition} Jalview uses the visible part of each alignment view to define
+\subsubsection{Choosing which part of the Alignment is used for Structural
+Superposition} Jalview uses the visible part of each alignment view to define
which parts of each molecule are to be superimposed. Hiding a column in a view
used for superposition will remove that correspondence from the set, and will
exclude it from the superposition and RMSD calculation.
\end{center}
\end{figure}
-\exercise{Aligning structures using the ferredoxin
-sequence alignment.}{\label{superpositionex}
+\exercise{Aligning Structures using the Ferredoxin
+Sequence Alignment}{\label{superpositionex}
\exstep{Continue with the Jalview project created in exercise
\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
the small section and with the whole alignment. Which view do you think give the
best 3D superposition, and why ?} }
-\subsection{Colouring structure data associated with multiple alignments and views}
-Normally, the original view from which a particular structure view was
+\subsection{Colouring Structure Data Associated with Multiple Alignments and
+Views} Normally, the original view from which a particular structure view was
opened will be the one used to colour structure data. If alignments involving
sequences associated with structure data shown in a Jmol have multiple views, Jalview gives you full control
over which alignment, or alignment view, is used to colour the structure
\end{center}
\end{figure}
-\subsubsection{Colouring complexes}
+\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
The ability to control which multiple alignment view is used to colour
structural data is essential when working with data relating to
evolutionary history, and a complete picture of functional variation can
only be gained by integrating data from different alignments on the same
structure view. An example of this is shown in Figure
-\ref{mviewalcomplex}, based on data from Song et. al\footnote{Structure of
+\ref{mviewalcomplex}, based on data from Song et. al.\footnote{Structure of
DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Jikui Song, Olga Rechkoblit, Timothy H. Bestor, and Dinshaw J. Patel.
{\sl Science} 2011 {\bf 331} 1036-1040
\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
\end{center}
\end{figure}
-\exercise{Colouring a protein complex to explore domain-domain interfaces}{\label{dnmtcomplexex}
+\exercise{Colouring a Protein Complex to Explore Domain-Domain
+Interfaces}{\label{dnmtcomplexex}
\exstep{Download the PDB file at
-\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. This
-is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA server.}
+\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
+
+This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
+server.}
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
free memory available.
{\sl Use the following webstart link:
-\href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}}.}
+
+\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}}
\exstep{Retrieve the following
{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
\exstep{Drag the structure you downloaded in
in the structure.}}
\exstep{Save your work as a Jalview project and verify that it can be opened again by starting another Jalview Desktop instance, and dragging the saved project into the desktop window.}
-{\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
-you notice any strange behaviour when trying out this exercise, it may be a
-bug (see
-\href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
-for one relating to highlighting of positions in the alignment window).} }
+% {\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
+% you notice any strange behaviour when trying out this exercise, it may be a
+% bug (see
+% \href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
+% for one relating to highlighting of positions in the alignment window).}
+}
-\section{Analysis of alignments}
+\section{Analysis of Alignments}
\label{alignanalysis}
Jalview provides support for sequence analysis in two ways. A number of
analytical methods are `built-in', these are accessed from the {\sl Calculate}
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\includegraphics[width=3in]{images/PCA3.pdf}
-\caption{{\bf PCA Analysis} }
+\caption{{\bf PCA Analysis.} }
\label{PCA}
\end{center}
\end{figure}
the partitioned tree and the points in the PCA plot.
} }
-\subsubsection{PCA data export}
+\subsubsection{PCA Data Export}
Although the PCA viewer supports export of the current view, the plots produced
are rarely suitable for direct publication. The PCA viewer's {\sl File} menu
includes a number of options for exporting the PCA matrix and transformed points
\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 four built in models for calculating trees. Jalview can also load precalculated trees in Newick format (right).}
+\caption{{\bf Calculating Trees} Jalview provides four built in models 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}
+\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
+groups in Jalview.}
\label{trees2}
\end{center}
\end{figure}
% 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{
\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}).}
+\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}).}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the diferences between the two trees, calculated using different methods.}
\caption{The Redundancy Removal dialog box opened from the edit menu. Sequences that exceed the current percentage identity threshold and are to be removed are highlighted in black.}
\end{figure}
-\exercise{Remove redundant sequences}{
-
-{\sl Note: Jalview 2.8 users - bugs in this version mean that the 'Unlinked leaves' markings will not be shown when sequences are removed during this exercise.}
+\exercise{Remove Redundant Sequences}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
}
-\subsection{Subdividing the alignment according to specific mutations}
+\subsection{Subdividing the Alignment According to Specific Mutations}
It is often necessary to explore variations in an alignment that may correlate
with mutations observed in a particular region; for example, sites exhibiting
colourschemes can then be used to reveal any associated pattern of sequence
variation across the whole alignment.
-\subsection{Automated annotation of Alignments and Groups}
+\subsection{Automated Annotation of Alignments and Groups}
On loading a sequence alignment, Jalview will normally\footnote{Automatic
annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
Sequence logos can be enabled by default for all new alignments {\sl via} the
Visual tab in the Jalview desktop's preferences dialog box.
-\exercise{Group conservation analysis}{
+\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{Create a new view, and ensure the annotation panel is displayed, and
a range of bioinformatics analysis tasks. }
\parbox[c]{1.75in}{\includegraphics[width=1.65in]{images/wsmenu.pdf}}
-\subsection{One-way web services}
+\subsection{One-Way Web Services}
-There are three types of one way service in jalview. Database services,
+There are two types of one way service in Jalview. Database services,
which were introduced in in Section \ref{fetchseq}, provide sequence and
alignment data. They can also be used to add sequence IDs to an alignment
imported from a local file, prior to further annotation retrieval, as described
in Section \ref{featuresfromdb}. A second type of one way service is provided
by Jalview's DAS sequence feature retrieval system, which is described
-in Section \ref{dasfretrieval}. The final type of one way service are sequence
-and ID submission services, exemplified by the `Envision2 Services' provided
-by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
-INtegration. Please see http://www.enfin.org for more information. }.
-
-\subsubsection{One-way submission services}
-Jalview can use the system's web browser to submit sets of sequences and
-sequence IDs to web based applications. Single sequence IDs can be passed to
-a web site using the user definable URL links listed under the {\sl
-Links} submenu of the sequence ID popup menu. These are configured
-in the {\sl Connections} tab of the {\sl Preferences} dialog box.
-
-The Envision 2 services presented in the webservice menu provides are the first
-example of one-way services where multiple sequences or sequence IDs can be
-sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
-provides two sub-menus that enable you to submit the sequences or IDs
-associated with the alignment or just the currently selected sequences to one
-of the Envision2 workflows. Selecting any one will open a new browser window on
-the Envision2 web application. The menu entries and their tooltips provide
-details of the Envision2 workflow and the dataset set that will be submitted
-({\sl i.e.} the database reference type, or associated sequence subset). Please
-note, due to technical limitations, Jalview can currently only submit small
-numbers of sequences to the workflows - if no sequence or ID submissions are
-presented in the submenus, then try to select a smaller number of sequences to
-submit.
+in Section \ref{dasfretrieval}.
+% The final type of one way service are sequence
+% and ID submission services.
+% exemplified by the `Envision2 Services' provided
+% by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
+% INtegration. Please see http://www.enfin.org for more information. }.
+
+% \subsubsection{One-way submission services}
+% Jalview can use the system's web browser to submit sets of sequences and
+% sequence IDs to web based applications. Single sequence IDs can be passed to
+% a web site using the user definable URL links listed under the {\sl
+% Links} submenu of the sequence ID popup menu. These are configured
+% in the {\sl Connections} tab of the {\sl Preferences} dialog box.
+%
+% The Envision 2 services presented in the webservice menu provides are the first
+% example of one-way services where multiple sequences or sequence IDs can be
+% sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
+% provides two sub-menus that enable you to submit the sequences or IDs
+% associated with the alignment or just the currently selected sequences to one
+% of the Envision2 workflows. Selecting any one will open a new browser window on
+% the Envision2 web application. The menu entries and their tooltips provide
+% details of the Envision2 workflow and the dataset set that will be submitted
+% ({\sl i.e.} the database reference type, or associated sequence subset). Please
+% note, due to technical limitations, Jalview can currently only submit small
+% numbers of sequences to the workflows - if no sequence or ID submissions are
+% presented in the submenus, then try to select a smaller number of sequences to
+% submit.
\subsection{Remote Analysis Web Services}
Remote analysis services enable Jalview to use external computational
progress of running jobs.
-\subsection{JABA Web Services for sequence alignment and analysis}
+\subsection{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
%%\item Learn how to install JABA services and configure Jalview to access them
%%\end{list}
-\subsection{Changing the Web Services menu layout}
+\subsection{Changing the Web Services Menu Layout}
\label{changewsmenulayout}
If you are working with a lot of different JABA services, you may wish to change
the way Jalview lays out the web services menu. You can do this from the Web
\exercise{Changing the Layout of the Web Services Menu}{
\label{changewsmenulayoutex}
\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment windowÔøΩs {\sl Web Service} menu.}
+current layout of the alignment window's {\sl Web Service} menu.}
\exstep{Open the preferences dialog box and select the web services tab.}
\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
the {\sl Enable Enfin Services} checkboxes.}
Test results from JABAWS are reported on Jalview's console output (opened from
the Tools menu). Tests are re-run every time Jalview starts, and when the
-[Refresh] button is pressed on the Jalview JABAWS configuration panel.
+[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.
-\subsubsection{Resetting the JABA services setting to their defaults}
+\subsubsection{Resetting the JABA Services Setting to their Defaults}
Once you have configured a JABAWS server and selected the OK button of the
preferences menu, the settings will be stored in your Jalview preferences file,
along with any preferences regarding the layout of the web services menu. If
you should ever need to reset the JABAWS server list to its defaults, use the
`Reset Services' button on the Web Services preferences panel.
-\subsection{Running your own JABA server}
+\subsection{Running your own JABA Server}
You can download and run JABA on your own machine using the `VMWare' or
VirtualBox virtual machine environments. If you would like to learn how to do
this, there are full instructions at the
\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
-\exercise{Installing a JABA Virtual Machine on your computer}{
+\exercise{Installing a JABA Virtual Machine on your Computer}{
\label{jabawsvmex}{\sl This tutorial will demonstrate the simplest way of
installing JABA on your computer, and configuring Jalview so it can access the JABA services.
this will begin with `http:' and end with `/jabaws''.}
}
-\exercise{Configuring Jalview to access your new JABAWS virtual appliance}{
+\exercise{Configuring Jalview to Access your new JABAWS Virtual Appliance}{
\label{confnewjabawsappl}
\exstep{Start Jalview (If you have not done so already).}
\exstep{Enable the Jalview Java Console by selecting its option from the Tools
\parbox[c]{2in}{\includegraphics[width=2in]{images/ws3.pdf}}
\caption{{\bf Multiple alignment via web services} The appropriate method is
selected from the menu (left), a status box appears (centre), and the results
-appear in a new window (right)}
+appear in a new window (right).}
\label{webservices}
\end{center}
\end{figure}
provided by ClustalW in this case is effectively a simple form of profile
alignment.
-\subsubsection{Alignments of sequences that include hidden regions}
+\subsubsection{Alignments of Sequences that include Hidden Regions}
If the view or selected region that is submitted for alignment contains hidden
regions, then {\bf only the visible sequences will be submitted to the service}.
}
-\subsection{Customising the parameters used for alignment}
+\subsection{Customising the Parameters used for Alignment}
JABA web services allow you to vary the parameters used when performing a
bioinformatics analysis. For JABA alignment services, this means you are
\end{list}
-\subsubsection{Getting help on the parameters for a service}
+\subsubsection{Getting Help on the Parameters for a Service}
Each parameter available for a method usually has a short description, which
-jalview will display as a tooltip, or as a text pane that can be opened under
+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
pre-defined sets of parameters suited for particular types of alignment
problem. For instance, the Muscle service provides the following presets:
\begin{list}{$\bullet$}{}
-\item Huge
+\item Large alignments (balanced)
\item Protein alignments (fastest speed)
\item Nucleotide alignments (fastest speed)
\end{list}
The presets are displayed in the JABA web services submenu, and can also be
accessed from the parameter editing dialog box, which is opened by selecting
-the `{\sl Edit settings and run ...}' option from the web serviceÔøΩs menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web services menu. If you have used
a preset, then it will be mentioned at the beginning of the job status file shown
in the web service job progress window.
can handle, then an error message will be shown informing you of the maximum
number allowed by the server.
-\subsection{User defined Presets}
+\subsection{User Defined Presets}
Jalview allows you to create your own presets for a particular service. To do
this, select the `{\sl Edit settings and run ...}' option for your service,
which will open a parameter editing dialog box like the one shown in Figure
\label{jwsparamsdialog} }
\end{figure}
-\subsubsection{Saving parameter sets}
+\subsubsection{Saving Parameter Sets}
When creating a custom parameter set, you will be asked for a file name to save
it. The location of the file is recorded in the Jalview user preferences in the
same way as a custom alignment colourscheme, so when Jalview is launched again,
% }
% }
-\section{Protein alignment conservation analysis}
+\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
score developed by Manning et al. in 2008.\footnote{SMERFS Score Manning et al. {\sl BMC
Bioinformatics} 2008, {\bf 9} 51 \href{http://dx.doi.org/10.1186/1471-2105-9-51}{doi:10.1186/1471-2105-9-51}}
-\subsubsection{Enabling and disabling AACon calculations}
+\subsubsection{Enabling and Disabling AACon Calculations}
When the AACon Calculation entry in the {\sl Web Services $\Rightarrow$
Conservation} menu is ticked, AACon calculations will be performed every time
the alignment is modified. Selecting the menu item will enable or disable
automatic recalculation.
-\subsubsection{Configuring which AACon calculations are performed}
+\subsubsection{Configuring which AACon Calculations are Performed}
The {\sl Web Services $\Rightarrow$ Conservation $\Rightarrow$ Change AACon
Settings ...} menu entry will open a web services parameter dialog for the
currently configured AACon server. Standard presets are provided for quick and
AACon settings for an alignment are saved in Jalview projects along with the
latest calculation results.
-\subsubsection{Changing the server used for AACon calculations}
+\subsubsection{Changing the Server used for AACon Calculations}
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
{\sl Note: you may want to keep this data for use in exercise \ref{viewannotfileex}.}
}
-}
+\exstep{
+In the original alignment that you loaded in step 1, {\bf select all} sequences,
+then open the {\bf Sequence ID $\Rightarrow$ Selection } submenu and select the
+{\bf Add Reference Annotation} option.
+
+The JNet predictions for the sequences should now be visible in the original
+alignment.} }
\section{Protein Disorder Prediction}
\label{protdisorderpred}
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
-\subsection{Disorder prediction results}
+\subsection{Disorder Prediction Results}
Each service operates on sequences in the alignment to identify regions likely
to be unstructured or flexible, or alternately, fold to form globular domains.
As a consequence, disorder predictor results include both sequence features and
\end{center}
\end{figure}
-\subsubsection{Navigating large sets of disorder predictions}
+\subsubsection{Navigating Large Sets of Disorder Predictions}
{\bf Figure \ref{alignmentdisorderannot}} shows a single sequence annotated with
a range of disorder predictions. Disorder prediction annotation rows are
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/disorderpredannot.pdf}
-\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disorderd regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
+\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A
+zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disordered regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
\label{alignmentdisorderannot}
\end{center}
\end{figure}
-\subsection{Disorder predictors provided by JABAWS 2.0}
+\subsection{Disorder Predictors provided by JABAWS 2.0}
For full details of each predictor and the results that Jalview can display,
please consult
\href{http://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's
by default, but can be shown by right-clicking on the alignment
annotation panel and selecting \textbf{Show hidden annotation}.
+\exercise{Protein Disorder Prediction}{
+\label{protdispredex}
+
+\exstep{Open the alignment at
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
+
+\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services
+$\Rightarrow$ Disorder Prediction } submenu.}
+
+\exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
+IDs} to retrieve all the PDB structures for the sequences.}
+
+\exstep{Open and align
+the structures for all sequences.
+
+{\sl Hint: see \ref{viewAllStructures} to see how to do this.}}
+
+\exstep{Compare the disorder predictions to the structure data by mapping any
+available temperature factors to the alignment {\sl via} the {\sl Sequence ID
+Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
+
+\exstep{Apply the IUPred disorder prediction method}
+\exstep{Use the {\sl Per
+sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
+the sequences by the long and short disorder predictors.
+Do the two methods agree with the structure ?}}
+
\section{Features and Annotation}
\label{featannot}
Features and annotations are additional information that is overlaid on the sequences and the alignment. Generally speaking, annotations are associated with columns in the alignment. Features are associated with specific residues in the sequence.
sequence features, whilst webservices like JNet (see \ref{jpred} above) can be used to analyse a given sequence or alignment and generate annotation for it.
-\subsection{Creating sequence features}
+\subsection{Creating Sequence Features}
Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialogue box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
\begin{figure}[htbp]
\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 it's own sequence.
+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}
+\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
Features file format for the import of sequence annotation. Features and
alignment annotation are also extracted from other formats such as Stockholm,
and AMSA. URL links may also be attached to features. See the online
-documentation for more details of the additional capabilities of the jalview
+documentation for more details of the additional capabilities of the Jalview
features file.
-\exercise{Creating features}{
+\exercise{Creating Features}{
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in iron binding so we will create them as features. Navigate to column 97, sequence 1. Select the entire column by clicking in the ruler bar. Then right-click on the selection to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}. A dialogue box will appear.
}
\exstep{
now displayed. Close the sequence feature settings box by clicking OK or
Cancel.} }
-\subsection{Creating user defined annotation}
+\subsection{Creating User Defined Annotation}
Annotations are properties that apply to the alignment as a whole and are visualized on rows in the annotation panel.
To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}). A dialogue box appears. Enter the label to use for this row and a new row will appear.
\end{center}
\end{figure}
-\exercise{Annotating alignments}{
+\exercise{Annotating Alignments}{
\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} to bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}. Enter ``Iron binding site" and click OK. A new, empty, row appears.
}
\exstep{
\label{viewannotfileex}\exstep{Recover or recreate the secondary structure
prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row. Note the {\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the annotation. } }
-\section{Importing features from databases}
+\section{Importing Features from Databases}
\label{featuresfromdb}
Jalview supports feature retrieval from public databases either directly or {\sl
via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}).
-It includes built in parsers for Uniprot and EMBL records retrieved from the
-EBI. Sequences retrieved from these sources using the sequence fetcher (see
+It includes built in parsers for Uniprot and ENA (or EMBL) records retrieved
+from the EBI. Sequences retrieved from these sources using the sequence fetcher (see
Section \ref{fetchseq}) will already possess features.
\subsection{Sequence Database Reference Retrieval}
do not match the coordinate system from which the features were defined, then
the features will be displayed incorrectly.
-\subsubsection{Viewing and exporting a sequence's database annotation}
+\subsubsection{Viewing and Exporting a Sequence's Database Annotation}
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
\parbox[c]{3in}{
\centerline{\includegraphics[width=2.2in]{images/seqdetailsreport.pdf}}}
-\subsubsection{Automatically discovering a sequence's database references}
+\subsubsection{Automatically Discovering a Sequence's Database References}
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
Following DAS feature retrieval, the {\sl Feature Settings} panel takes on a
slightly different appearance (Figure \ref{das} (right)). Each data source is
listed and groups of features from one data source can be selected/deselected
-by checking the labeled box at the top of the panel.
+by checking the labelled box at the top of the panel.
-\subsubsection{The Fetch Uniprot IDs 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 to ensure that features retrieved from the DAS source are rendered at the correct position.
-\subsubsection{Rate of feature retrieval}
+\subsubsection{Rate of Feature Retrieval}
Feature retrieval can take some time if a large number of sources is selected and if the alignment contains a large number of sequences. This is because Jalview only queries a particular DAS source with one sequence at a time, to avoid overloading it. As features are retrieved, they are immediately added to the current alignment view. The retrieved features are shown on the sequence and can be customised as described previously.
-\exercise{Retrieving features with DAS}{
+\exercise{Retrieving Features with DAS}{
\label{dasfeatretrexcercise}
\exstep{Load the alignment at
\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
-the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click OK. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment. } \exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Sequence Feature Settings window. }
-\exstep{Move the mouse over the sequence ID panel. Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
-\exstep{Search through the alignment to find a feature with a link symbol next to it. Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
+the {\sl DAS Settings} tab. A long list of available DAS sources is listed.
+Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click.
+A window may prompt whether you wish Jalview to fetch DAS features. Click {\sl
+Yes}.
+Jalview will start retrieving features. As features become available they will be mapped onto the alignment. }
+\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button.
+Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip.
+Close the Sequence Feature Settings window. }
+\exstep{Move the mouse over the sequence ID panel.
+Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
+\exstep{Search through the alignment to find a feature with a link symbol next to it.
+Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
\exstep{
}
}
-\subsection{Colouring features by score or description
-text}
+\subsection{Colouring Features by Score or Description
+Text}
\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
style and a greater than ($>$) or less than ($<$) symbol to indicate when a
threshold has been defined.
-\subsection{Using features to re-order the alignment}
+\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
then only features found in that region of the alignment will be used to
create the new alignment ordering.
-\exercise{Shading and sorting alignments using sequence features}{
-\label{shadingorderingfeatsex}
-\exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
-}
-\exstep{Open the
-feature settings panel, and, after first clearing the current
-selection, press the {\em Seq Sort by Density} button a few times.}
-\exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
-scores for the protein sequences in the alignment.
-{\sl Hint: the nickname for the das source is `KD$\_$hydrophobicity'.}}
-\exstep{Change the feature settings so only the hydrophobicity features are
-displayed. Mouse over the annotation and also export and examine the GFF and
-Jalview features file to better understand how the hydrophobicity measurements
-are recorded.}
-\exstep{Apply a {\sl Graduated Colour} to the hydrophobicity annotation to
-reveal the variation in average hydrophobicity across the alignment.}
-\exstep{Select a range of alignment columns, and use one of the sort by feature buttons to order the alignment according to that region's average
-hydrophobicity.}
-\exstep{Save the alignment as a project, for use in exercise
-\ref{threshgradfeaturesex}.} }
-
-\exercise{Shading alignments with combinations of graduated feature
-colourschemes}{
-\label{threshgradfeaturesex}
-\exstep{Reusing the annotated alignment from exercise
-\ref{shadingorderingfeatsex}, experiment with the colourscheme threshold to
-highlight the most, or least hydrophobic regions. Note how the {\sl Colour} icon for the {\sl Feature Type} changes when you change the threshold type and press OK.}
-\exstep{Change the colourscheme so
-that features at the threshold are always coloured grey, and the most
-hydrophobic residues are coloured red, regardless of the threshold value
-({\em hint - there is a switch on the dialog to do this for you}).}
-\exstep{Enable the Uniprot {\em chain} annotation in the feature settings
-display and re-order the features so it is visible under the hydrophobicity
-annotation.}
-\exstep{Apply a {\sl Graduated Colour} to the {\em chain}
-annotation so that it distinguishes the different canonical names associated
-with the mature polypeptide chains.}
-\exstep{Export the alignment's sequence features using the Jalview and GFF file formats, to see how the different types of graduated feature
-colour styles are encoded. }
-}
+% \exercise{Shading and Sorting Alignments using Sequence Features}{
+% \label{shadingorderingfeatsex}
+%
+% This exercise is currently not included in the tutorial because no DAS servers
+% currently exist that yield per-residue features for any Uniprot sequence.
+%
+% \exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
+% }
+% \exstep{Open the
+% feature settings panel, and, after first clearing the current
+% selection, press the {\em Seq Sort by Density} button a few times.}
+% \exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
+% scores for the protein sequences in the alignment.
+% {\sl Hint: the nickname for the das source is `KD$\_$hydrophobicity'.}}
+% \exstep{Change the feature settings so only the hydrophobicity features are
+% displayed. Mouse over the annotation and also export and examine the GFF and
+% Jalview features file to better understand how the hydrophobicity measurements
+% are recorded.}
+% \exstep{Apply a {\sl Graduated Colour} to the hydrophobicity annotation to
+% reveal the variation in average hydrophobicity across the alignment.}
+% \exstep{Select a range of alignment columns, and use one of the sort by feature buttons to order the alignment according to that region's average
+% hydrophobicity.}
+% \exstep{Save the alignment as a project, for use in exercise
+% \ref{threshgradfeaturesex}.} }
+%
+% \exercise{Shading alignments with combinations of graduated feature
+% colourschemes}{
+% \label{threshgradfeaturesex}
+% \exstep{Reusing the annotated alignment from exercise
+% \ref{shadingorderingfeatsex}, experiment with the colourscheme threshold to
+% highlight the most, or least hydrophobic regions. Note how the {\sl Colour} icon for the {\sl Feature Type} changes when you change the threshold type and press OK.}
+% \exstep{Change the colourscheme so
+% that features at the threshold are always coloured grey, and the most
+% hydrophobic residues are coloured red, regardless of the threshold value
+% ({\em hint - there is a switch on the dialog to do this for you}).}
+% \exstep{Enable the Uniprot {\em chain} annotation in the feature settings
+% display and re-order the features so it is visible under the hydrophobicity
+% annotation.}
+% \exstep{Apply a {\sl Graduated Colour} to the {\em chain}
+% annotation so that it distinguishes the different canonical names associated
+% with the mature polypeptide chains.}
+% \exstep{Export the alignment's sequence features using the Jalview and GFF file formats, to see how the different types of graduated feature
+% colour styles are encoded. }
+% }
\section{Working with DNA}
\label{workingwithnuc}
Jalview was originally developed for the analysis of protein sequences, but
sequence fetcher (see Section \ref{fetchseq}) are also parsed in order to
identify codon regions and extract peptide products. Furthermore, Jalview
records mappings between protein sequences that are derived from regions of a
-nucleotide sequence. Mappings are used to to transfer annotation between
+nucleotide sequence. Mappings are used to transfer annotation between
nucleic acid and protein sequences, and to dynamically highlight regions in
one sequence that correspond to the position of the mouse pointer in another.
%TODO Working with Nucleic acid sequences and structures.
for nucleotide alignment. Generally, all will work, but some may be more suited
to your purposes than others. We also note that none of these include
support for taking RNA secondary structure prediction into account when aligning
-sequences. We expect that in the future, Jalview will fully support secondary
-structure aware RNA alignment.
-
+sequences (but will be providing services for this in the future!)
\begin{table}{}
\centering
\begin{tabular}{|l|c|l|}
}
-\subsection{Coding regions from EMBL records}
+\subsection{Coding Regions from EMBL Records}
Many EMBL records that can be retrieved with the sequence fetcher contain exons.
Coding regions will be marked as features on the EMBL nucleotide sequence, and
\subsubsection{Retrieval of Protein or DNA Cross References}
The {\sl Calculate $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the protein product(s).
-\subsubsection{Retrieval of protein DAS features on coding regions}
+\subsubsection{Retrieval of Protein DAS Features on Coding Regions}
The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments. This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig. Jalview will use the Uniprot accession numbers associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using the coding region location.
\end{center}
\end{figure}
-\exercise{Visualizing protein features on coding regions}
+\exercise{Visualizing Protein Features on Coding Regions}
{
-\exstep{Use the sequence fetcher to retrieve EMBL record V00488.}
+\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the alignment view format to Wrapped mode so the distinct exons can be seen.}
-\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for V00488 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
+\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for D49489 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
\exstep{Mouse over the features retrieved, note that they have been mapped onto the coding regions, and in some cases broken into several parts to cover the distinct exons.}
\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculate $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
}
% \subsection{Working with Modeller files}
% \subsection{Using local PDB files}
% \section{Pairwise alignments}
+\subsection{Working with RNA}
+Jalview allows the creation of RNA secondary structure annotation, and includes
+the VARNA secondary structure viewer for the display of RNA base pair diagrams.
+It also allows the extraction of RNA secondary structure from 3D data when
+available.
+
+\subsection{Performing RNA Secondary Structure Predictions}
+Secondary structure consensus calculations can be performed by enabling the
+VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+Structure} menu. These consensus structures are created by analysing the
+covariation patterns in all visible sequences on the alignment. For more
+information see the VIENNA documentation.
+
+\begin{figure}[htbp]
+\begin{center}
+\label{rnaviennaservice}
+\includegraphics[width=5in]{images/rnaViennaServiceWindow.pdf}
+
+\caption{Secondary structure consensus calculations can be performed by enabling the
+VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+Structure} menu.}
+
+\end{center}
+\end{figure}
+
+\begin{figure}[htbp]
+\begin{center}
+\label{rnaviennaaltpairs}
+\includegraphics[width=5in]{images/rnaViennaAlternateProbs.pdf}
+
+\caption{VIENNA can calculate alternate RNA base pairing probabilities. These
+are shown in Jalview as tool-tips on the RNA secondary structure probability
+score.}
+
+\end{center}
+\end{figure}
+
+
+\exercise{Viewing RNA Structures}{
+\label{viewingrnaex}
+
+\exstep{Import RF00162 from Rfam (Full).}
+\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
+the secondary structure annotation provided by Rfam.}
+\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
+$\Rightarrow$ RNA Secondary Structure}.
+
+ Explore the difference between trimmed and untrimmed views for the
+ structure.
+}
+\exstep{Add and link a Jmol structure view
+for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
+structure along-side the consensus structure for the alignment by adding
+reference annotation from the 3D structure.
+
+{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
+Structure} preferences to obtain RNA secondary structure annotation from PDB
+files.}}
+
+\exstep{Perform a secondary structure prediction. Enable the VIENNA consensus
+calculation via the {\sl Web Services} menu. Compare this with the annotation
+line provided by Rfam.}
+
+\exstep{Edit the VIENNA calculation settings to show
+Base Pair probabilities.
+
+Explore how editing the alignment affects the consensus
+calculation.} }
+
- \end{document}
+\end{document}
git://source.jalview.org / jalview-manual.git / blobdiff