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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>Sequence Fetcher</title>
</head>
<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>
- <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"
- menu on the main desktop in order to retrieve sequences as a new
- alignment, or opened via the "File" menu of an existing alignment
- to import additional sequences. There may be a short delay when the sequence fetcher is first opened,
- 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
- 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>
- <img src="selectfetchdb.gif" align="left" alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
- <p>Since Jalview 2.8, the
- available databases are shown as a tree in a popup dialog box. The
- 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
- "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><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>Sequence Fetcher</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)
- 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>
- SOAP-based services provided by the European Bioinformatics Institute.<br>
- Nucleic Acids Res. 33(1):W25-W28 (2005) <br>
- <br>
+ <p>
+ Jalview can retrieve sequences from certain databases using either
+ the 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" menu on the main desktop in order to retrieve
+ sequences as a new alignment, or opened via the "File"
+ menu of an existing alignment to import additional sequences. There
+ may be a short delay when the sequence fetcher is first opened,
+ whilst Jalview compiles the list of available sequence datasources
+ from the currently defined DAS server registry.</p>
+ <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>
+ <img src="selectfetchdb.gif" align="left"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
+ >
+ <p>Since Jalview 2.8, the available databases are shown as a tree
+ in a popup dialog box. The 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, <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>
+ <strong>Fetching from The PDB with the EMBL-EBI PDBe Search
+ Interface</strong>
+ </p>
+ <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> SOAP-based services provided by the European
+ Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
+ (2005) <br> <br>
</p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff