- <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 a range of sequence, 3D
+ structure, genomic and domain family databases provided by EMBL-EBI.</p>
+ <p>The Sequence Fetcher 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 contacts each database's web API.</p>
+ <p>
+ Every time a new fetcher is opened, you will need to <strong>select
+ the database you want to retrieve sequences</strong> from the database
+ chooser.
+ </p>
+ <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+ <p>
+ The databases are shown as a tree, and ordered alphabetically;
+ tooltips are shown if you mouse over some sources, explaining what
+ the database will retrieve. You can select one by using the up/down
+ arrow keys and hitting return, or by double clicking with the mouse.
+ </p>
+ <p>Once you have selected a sequence database, its fetcher dialog
+ will open. Jalview provides two types of dialog:</p>
+ <ol>
+ <li><strong>The Free-text Search Interface</strong> <br />Free-text
+ search clients are provided for PDB (Since 2.9), and UniProt
+ (Since 2.10). They provide access to each database's own query
+ system, enabling you to retrieve data by accession, free text
+ description, or any other type of supported field. For full
+ details, see each client's help page:
+ <ul>
+ <li><a href="pdbsequencefetcher.html">PDB Sequence
+ Fetcher</a></li>
+ <li><a href="uniprotsequencefetcher.html">UniProt
+ Sequence Fetcher</a></li>
+ </ul></li>
+ <li><strong>Accession based sequence retrieval</strong> <br />
+
+ <img src="seqfetcher.gif" align="center"
+ alt="The Jalview Sequence Fetcher Dialog Box"><br /> To
+ retrieve sequences, simply <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.</li>
+ </ol>
+
+ <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>