<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>
git://source.jalview.org / jalview.git / blobdiff