<body>
<p><strong>Sequence Fetcher</strong></p>
<p>Jalview can retrieve sequences from certain databases using either the
-WSDBFetch service provided by the European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
+DBFetch service provided by the EMBL European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
<img src="seqfetcher.gif" align="center"
alt="The Jalview Sequence Fetcher Dialog Box">
<p>The Sequence Fetcher dialog box can be opened via the "File"
whilst Jalview compiles the list of available sequence datasources from the
currently defined DAS server registry.
</p>
- <p>First, select the database you want to retrieve sequences from
+ <p>First, <strong>select the database you want to retrieve sequences from</strong>
by clicking the button labeled 'Select database retrieval source'. If
a database source is already selected, then the button's label will
change to show the currently selected database.</p>
databases are ordered alphabetically, and if there are many sources
for the same type of sequence identifier, they will be grouped
together in a sub-branch branch labeled with the identifier.</p>
- <p>Once you have selected the sequence database using the popup dialog box, enter
- one or more accession ids (as a semi-colon separated list), or press the
+ <p>Once you have selected the sequence database using the popup dialog box, <strong>enter
+ one or more accession ids</strong> (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the currently selected database into the retrieval box.
Finally, press "OK" to initiate the retrieval.</p>
- <p>Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequence data. </p>
- <p><strong>Specifying chains for PDB IDs</strong>
- If you are retrieving sequences from the PDB, you can retrieve
- specific chains by appending a colon and the chain id to the PDB
- id. For example :<br/><pre> 1GAQ:A</pre>
+ <p>
+ <strong>Fetching from The PDB with the EMBL-EBI PDBe Search
+ Interface</strong>
</p>
- <p>
- <strong>Only retrieving part of a sequence</strong> DAS sources
- (indicated by a "<em>(DAS)</em>") allow a range to be
- specified in addition to a sequence ID. To retrieve 50 residues
- starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
- DAS server, you would enter "'P73137:35,84'.<br/><em>Full support for DAS range queries was introduced in Jalview 2.8</em>
- </p>
-
-<p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM)
+ <p>
+ Since Jalview 2.9, selecting PDB as the sequence database will open
+ the <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> for
+ discovering and retrieving structures.
+ </p>
+ <p>
+ <strong>Only retrieving part of a sequence</strong>
+ </p>
+ <p>
+ DAS sources (indicated by a "<em>(DAS)</em>") allow a
+ range to be specified in addition to a sequence ID. To retrieve 50
+ residues starting at position 35 in UNIPROT sequence P73137 using
+ the UNIPROT DAS server, you would enter "'P73137:35,84'.<br />
+ <em>Full support for DAS range queries was introduced in
+ Jalview 2.8</em>
+ </p>
+
+ <p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PFAM, and RFAM)
in work for publication, please cite:</p>
<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>
</head>
<body>
<p><strong>Split Frame Views</strong></p>
-<p/></p>Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are
-linked, with these features supported:
-<ul>
-<li>mouseover or scrolling of either alignment is followed by the other (unless you turn off <strong><a href="../menus/alwview.html">"View→Automatic Scrolling"</a></strong>)</li>
-<li>on selecting rows, columns or regions in one alignment, the corresponding selection is made in the other</li>
-<li>sequence ordering in one alignment (using the cursor, or <strong><a href="../calculate/sorting.html">"Calculate→Sort")</a></strong> is also applied to the other</li>
-<li>editing (gap insertion / deletion) in the protein alignment is reflected in the cDNA (but not vice versa)</li>
-<li>on <strong><a href="../calculations/tree.html">"Calculate Tree"</a></strong> in either alignment, grouping, colouring and sorting by tree are applied to both</li>
-<li>the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong> menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue
-the same width as a DNA codon (so the alignments 'line up' vertically)</li>
-<li>menu option <strong>"View→Protein"</strong> (in the cDNA panel) or <strong>"View→Nucleotide"</strong> (in the protein panel) allows you to show or hide the complementary alignment</li>
-<li>you can adjust panel heights by dragging the divider between them using the mouse</li>
-<li>menu options <a href="menus/alwview.html"><strong>"View→New View / Expand Views / Gather Views"</strong></a> behave as for a normal alignment window, but always create new views
-as split frames</li>
-</ul>
-<p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
+ <p>
+ Jalview provides a special viewing mode to show Coding DNA (cDNA)
+ and protein product alignments as a split view, with cDNA above and
+ protein below. The two alignments are linked, allowing editing and
+ analysis to be performed at both the peptide and nucleotide level.
+ Linked protein alignments also have an additional
+ <strong>cDNA Consensus</strong> annotation row, showing the
+ distribution of codons at each column
+ of the protein alignment.
+ </p>
+ <p>
+ Split Frame views can be <a
+ href="#opensplit">created in a number of ways</a>. In the Jalview
+ Desktop, Split Frame views are saved in Jalview Projects, like any
+ other alignment view.
+ </p>
+ <p><strong>Operations supported in Split Frame Mode</strong></p>
+<p>Split Frame views allow the following:
+
+ <ul>
+ <li>Mouseover or scrolling of either alignment is followed by
+ the other (unless you turn off <strong><a
+ href="../menus/alwview.html">"View→Automatic
+ Scrolling"</a></strong>)
+ </li>
+ <li>On selecting rows, columns or regions in one alignment, the
+ corresponding selection is made in the other</li>
+ <li>Sequence ordering in one alignment (using the cursor, or <strong><a
+ href="../calculate/sorting.html">"Calculate→Sort")</a></strong> is
+ also applied to the other
+ </li>
+ <li>Editing (gap insertion / deletion) in the protein alignment
+ is reflected in the cDNA (but not vice versa)</li>
+ <li>Any trees imported or created with <strong><a
+ href="../calculations/tree.html">"Calculate Tree"</a></strong> on one of
+ the views allow both cDNA and Protein views to be grouped,
+ coloured or sorted.
+ </li>
+ <li>To allow for the different widths in cDNA and Protein
+ alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
+ menu option has an option 'Scale protein residues to codons'. This
+ option will make each protein residue the same width as a DNA
+ codon (so the alignments 'line up' vertically)
+ </li>
+ <li><strong>"View→Protein"</strong> (in the cDNA panel)
+ or <strong>"View→Nucleotide"</strong> (in the protein panel)
+ allows you to show or hide one or other of the linked alignment
+ panels.</li>
+ <li>Panel heights are adjusted dragging the divider between
+ them using the mouse</li>
+ <li><a href="menus/alwview.html"><strong>"View→New
+ View / Expand Views / Gather Views"</strong></a> behave as for a normal
+ alignment window, but always create new views as Split Frames</li>
+ </ul>
+ <p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
This consensus may reveal variation in nucleotides coding for conserved protein residues.</p>
-<p><strong>Opening a Split Frame View</strong></p>
+<a name="opensplit"/><p><strong>Opening a Split Frame View</strong></p>
<p>A Split Frame View can be opened in one of the following ways:</p>
<p><strong><em>Add Sequences</em></strong></p>
<p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
<li>Jalview reconstructs the alignment of its complement (in
this case, cDNA) by inserting gaps in the corresponding positions</li>
</ul>
- <p><strong>Reconstructed Alignments</strong>
- Reconstructed alignments are typically <em>not</em>
- the same as the alignment produced by aligning the complement
- sequence set directly with the external service. However, in the
- case of protein alignments, a reconstructed cDNA alignment is often
- more reliable than one calculated without coding information.
- Reconstructed cDNA alignments are also more informative than the
- original protein alignment when calculating phylogenetic trees or
- performing other kinds of molecular evolution analysis.
+ <p>
+ <a name="reconalignment" /><strong>Reconstructed Alignments</strong>
+ </p>
+ <p>
+ Reconstructed alignments are typically <em>not</em> the same as the
+ alignment produced by aligning the complement sequence set directly
+ with the external service. However, in the case of protein
+ alignments, a reconstructed cDNA alignment is often more reliable
+ than one calculated without coding information. Reconstructed cDNA
+ alignments are also more informative than the original protein
+ alignment when calculating phylogenetic trees or performing other
+ kinds of molecular evolution analysis.
</p>
<p>
<em>Split Frame Views were introduced in Jalview 2.9</em>
</ul>
</li>
<li>Jmol integration updated to Jmol v14.2.14</li>
- <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
+ <li>Import and export of Jalview alignment views as <a
+ href="">BioJSON</a></li>
<li>New alignment annotation file statements for
reference sequences and marking hidden columns</li>
- <li>Assign an alignment reference sequence to highlight
- variation</li>
+ <li>Reference sequence based alignment shading to
+ highlight variation</li>
<li>Select or hide columns according to alignment
annotation</li>
- <li>Find option for locating sequences by
- description</li>
+ <li>Find option for locating sequences by description</li>
<li>Conserved physicochemical properties shown in amino
acid conservation row</li>
<li>Alignments can be sorted by number of RNA helices</li>
- </ul>
- <em>Application</em>
+ </ul> <em>Application</em>
<ul>
- <li>Optional embedding of BioJSON data when exporting
- alignment figures to HTML</li>
- <li>New Export Settings dialog to control hidden region
- export in flat file generation</li>
<li>New cDNA/Protein analysis capabilities
<ul>
<li>Get Cross-References should open a Split Frame
</li>
<li>Use REST API to talk to Chimera</li>
- <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
-
- <li>Calculate UPGMA and NJ trees using sequence feature
- similarity</li>
+ <li>Selected regions in Chimera are highlighted in linked
+ Jalview windows</li>
<li>VARNA RNA viewer updated to v3.93</li>
- <li>VARNA views are saved in Jalview
- Projects</li>
- <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
-
- <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
- <li>change "View protein structure" menu option to "3D Structure ..."</li>
+ <li>VARNA views are saved in Jalview Projects</li>
+ <li>Pseudoknots displayed as Jalview RNA annotation can
+ be shown in VARNA</li>
<li>Make groups for selection uses marked columns as well
as the active selected region</li>
- <li>allow different similarity matrix calculations for
- tree building and PCA</li>
+ <li>Calculate UPGMA and NJ trees using sequence feature
+ similarity</li>
+ <li>New Export options
+ <ul>
+ <li>New Export Settings dialog to control hidden
+ region export in flat file generation</li>
- <li>Export alignment views for display with the <a
- href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
-
- <li>Export scrollable SVG in HTML page</li>
+ <li>Export alignment views for display with the <a
+ href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
- <li>Interactive free text and structured queries with the
- PDBe Search API for PDB data retrieval</li>
- <li>PDBe Search API based discovery and selection of PDB structures to
- view for a sequence set</li>
+ <li>Export scrollable SVG in HTML page</li>
+ <li>Optional embedding of BioJSON data when exporting
+ alignment figures to HTML</li>
+ </li>
+ <li>3D structure retrieval and display
+ <ul>
+ <li>Free text and structured queries with
+ the PDBe Search API</li>
+ <li>PDBe Search API based discovery and selection of
+ PDB structures for a sequence set</li>
+ </ul>
+ </li>
<li>JPred4 employed for protein secondary structure
predictions</li>
<li>Hide Insertions menu option to hide unaligned columns
for one or a group of sequences</li>
- <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
+ <li>Automatically hide insertions in alignments imported
+ from the JPred4 web server</li>
<li>(Nearly) Native 'Quaqua' dialogs for browsing file
system on OSX<br />LGPL libraries courtesy of <a
href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
</li>
+ <li>changed 'View nucleotide structure' submenu to 'View
+ VARNA 2D Structure'</li>
+ <li>change "View protein structure" menu option to "3D
+ Structure ..."</li>
+
</ul> <em>Applet</em>
<ul>
- <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
+ <li>New layout for applet example pages</li>
+ <li>New parameters to enable SplitFrame view (file2,enableSplitFrame,
+ scaleProteinAsCdna)</li>
<li>New example demonstrating linked viewing of cDNA and
Protein alignments</li>
- <li>New layout for applet example pages</li>
- </ul>
- <em>Development and deployment</em>
+ </ul> <em>Development and deployment</em>
+ <ul>
<li>Java 1.7 minimum requirement for Jalview 2.9</li>
<li>Include installation type and git revision in build
properties and console log output</li>
- <li>Github project and web URL for storing BioJsMSA
- Templates</li>
- <li>Jalview's unit tests now managed with TestNG</li></td>
+ <li>Jalview Github organisation, and new github site for
+ storing BioJsMSA Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li></ul></td>
<td>
<!-- <em>General</em>
<ul>
Jalview 2.9 has been in development since December 2014. In addition
to a multitude of bug fixes and minor improvements (both small, and
rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the manipulation of structural
- data.<br />For the full list of changes, see the <a
- href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ analysis of protein alignments and the retrieval and manipulation of
+ structural data.</p><p>For the full list of changes, see the
+ <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
</p>
<p>
<strong>Highlights in Jalview 2.9</strong>
-
<ul>
<li><strong>Visualisation, editing and analysis of
cDNA and Protein alignments</strong><br />A new <a
git://source.jalview.org / jalview.git / commitdiff