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>
- <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>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>
- 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.
+ 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;
+ 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.
- <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>
+ <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/>
+ <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>
+ <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>