<!--
- * 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.
*
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-<head>
-Database Reference Fetching
+<head>Database Reference Fetching
</head>
<p>
-<p><strong>Discovering Database References for Sequences</strong><br>
-Database references are associated with a sequence are displayed as a
-list in the tooltip shown when mousing over its sequence ID. Jalview
-uses references for the retrieval of <a
- href="../features/viewingpdbs.html">PDB structures</a> and <a
- href="../features/dasfeatures.html">DAS features</a>, and for
-retrieving sequence cross-references such as the protein products of a
-DNA sequence.</p>
-<p><strong>Initiating reference retrieval</strong><br>
-The application provides three ways to access the retrieval function. Either:
-<ul><li>select the <strong>Discover PDB IDs</strong> option from the structure submenu of the sequence's popup menu</li>
-<li>Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's <strong>Web Services</strong> menu:<ul>
-<li><em>Standard Databases</em> will fetch references from the EBI databases plus currently selected DAS sources</li>
-<li>The other entries submenus leading to lists of individual database sources that Jalview can access.</li></ul></li>
-<li>Answer 'Yes' when asked if you wish to retrieve database references for your sequences after initiating a DAS Sequence Feature fetch.</li>
-</ul>
+<p>
+ <strong>Discovering Database References for Sequences</strong><br>
+ Database references are associated with a sequence are displayed as a
+ list in the tooltip shown when mousing over its sequence ID. Jalview
+ uses references for the retrieval of <a
+ href="../features/viewingpdbs.html"
+ >PDB structures</a> and <a href="../features/dasfeatures.html">DAS
+ features</a>, and for retrieving sequence cross-references such as the
+ protein products of a DNA sequence.
+</p>
+<p>
+ <strong>Initiating reference retrieval</strong><br> The
+ application provides three ways to access the retrieval function.
+ Either:
+<ul>
+ <li>select the <strong>Discover PDB IDs</strong> option from the
+ structure submenu of the sequence's popup menu
+ </li>
+ <li>Choose one of the options from the 'Fetch DB Refs' submenu in
+ the alignment window's <strong>Web Services</strong> menu:
+ <ul>
+ <li><em>Standard Databases</em> will fetch references from
+ the EBI databases plus currently selected DAS sources</li>
+ <li>The other entries submenus leading to lists of individual
+ database sources that Jalview can access.</li>
+ </ul>
+ </li>
+ <li>Answer 'Yes' when asked if you wish to retrieve database
+ references for your sequences after initiating a DAS Sequence
+ Feature fetch.</li>
+</ul>
<p>Jalview discovers references for a sequence by generating a set
-of ID queries from the ID string of each sequence in the alignment. It
-then tries to query a subset of all the databases it can access in order to match
-the alignment sequence to any records retrieved from the database. If a
-match is found, then the sequence is annotated with that database's
-reference, and any cross-references that its records contain.</p>
-<p><strong>The Sequence Identification Process</strong><br>
-The method of accession id discovery is derived from the method which
-earlier Jalview versions used for Uniprot sequence feature retrieval,
-and was originally restricted to the identification of valid Uniprot
-accessions.<br>
-Essentially, Jalview will try to retrieve records from a subset of the databases
-accessible by the <a href="../features/seqfetch.html">sequence
-fetcher</a> using each sequence's ID string (or each string in the ID
-separated by the '∣' symbol).</p>
+ of ID queries from the ID string of each sequence in the alignment. It
+ then tries to query a subset of all the databases it can access in
+ order to match the alignment sequence to any records retrieved from
+ the database. If a match is found, then the sequence is annotated with
+ that database's reference, and any cross-references that its records
+ contain.</p>
+<p>
+ <strong>The Sequence Identification Process</strong><br> The
+ method of accession id discovery is derived from the method which
+ earlier Jalview versions used for Uniprot sequence feature retrieval,
+ and was originally restricted to the identification of valid Uniprot
+ accessions.<br> Essentially, Jalview will try to retrieve records
+ from a subset of the databases accessible by the <a
+ href="../features/seqfetch.html"
+ >sequence fetcher</a> using each sequence's ID string (or each string in
+ the ID separated by the '∣' symbol).
+</p>
<p>If a record (or set of records) is retrieved by any query derived
-from the ID string of a sequence, then the sequence is aligned to the
-ones retrieved to determine the correct start and end residue positions
-(which are displayed when the 'Show Full Sequence ID' option). This is
-important for the correct display of the location of any features
-associated with that database.</p>
+ from the ID string of a sequence, then the sequence is aligned to the
+ ones retrieved to determine the correct start and end residue
+ positions (which are displayed when the 'Show Full Sequence ID'
+ option). This is important for the correct display of the location of
+ any features associated with that database.</p>
<p>If the alignment reveals differences between the sequence in the
-alignment and the one in the record, then Jalview will assume that the
-aligned sequence is not the one in the retrieved record.</p>
-<p>In some cases, the ID used to retrieve records may be out
-of date and a dialog box will be opened indicating that a 100% match
-between the sequence and the record was identified, but the
-sequence name is different. In this case, the can be manually
-changed (by right clicking on the sequence ID and selecting <strong>Sequence→Edit
-Name</strong>).
+ alignment and the one in the record, then Jalview will assume that the
+ aligned sequence is not the one in the retrieved record.</p>
+<p>
+ In some cases, the ID used to retrieve records may be out of date and
+ a dialog box will be opened indicating that a 100% match between the
+ sequence and the record was identified, but the sequence name is
+ different. In this case, the can be manually changed (by right
+ clicking on the sequence ID and selecting <strong>Sequence→Edit
+ Name</strong>).
<ul>
- <li><em>Note</em><br>
- Please remember to save your alignment if either the start/end
- numbering, or the sequence IDs were updated during the ID
- retrieval process.</li>
+ <li><em>Note</em><br> Please remember to save your alignment
+ if either the start/end numbering, or the sequence IDs were updated
+ during the ID retrieval process.</li>
</ul>
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