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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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>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 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.
+ 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"
- 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>
+ <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
<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.
+ 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.
+ <br />
+ <em>If you have DAS sources enabled, then you may have several
+ sources for the same type of sequence identifier, and these will
+ be grouped together in a sub-branch branch labeled with the
+ identifier.</em>
</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>
<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>
+ When using DAS sources (indicated by a "<em>(DAS)</em>"),
+ you can append a range in addition to a sequence ID. For example, 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>
+ 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
git://source.jalview.org / jalview.git / blobdiff