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-<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>Database Reference Fetching
-</head>
-<p>
-<p>
- <strong>Discovering Database References for Sequences</strong><br>
- Database references associated with a sequence are displayed as an
- abbreviated list in the tooltip shown when mousing over its sequence
- ID, and can be viewed in full via the
- <a href="../io/exportseqreport.html">Sequence Details</a> window. .
- Jalview also uses references for the retrieval of
- <a href="../features/viewingpdbs.html">PDB structures</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>Structure Chooser...</strong> option from
- the Sequence ID 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 EBI
- databases appropriate for the sequence type (Nucleotide or Protein)</li>
- <li>The other entries submenus leading to lists of individual
- database sources that Jalview can access.</li>
- </ul>
- </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>
-<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>
-<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>).
-<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>
-</ul>
-<body></body>
-</html>
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