2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
22 <html xmlns="http://www.w3.org/1999/xhtml">
23 <head>Database Reference Fetching
27 <strong>Discovering Database References for Sequences</strong><br>
28 Database references associated with a sequence are displayed as an
29 abbreviated list in the tooltip shown when mousing over its sequence
30 ID, and can be viewed in full via the
31 <a href="../io/exportseqreport.html">Sequence Details</a> window. .
32 Jalview also uses references for the retrieval of
33 <a href="../features/viewingpdbs.html">PDB structures</a>, and for
34 retrieving sequence cross-references such as the protein products of a
38 <strong>Initiating reference retrieval</strong><br> The
39 application provides three ways to access the retrieval function.
42 <li>select the <strong>Structure Chooser...</strong> option from
43 the Sequence ID popup menu.
45 <li>Choose one of the options from the 'Fetch DB Refs' submenu in
46 the alignment window's <strong>Web Services</strong> menu:
48 <li><em>Standard Databases</em> will fetch references from EBI
49 databases appropriate for the sequence type (Nucleotide or Protein)</li>
50 <li>The other entries submenus leading to lists of individual
51 database sources that Jalview can access.</li>
55 <p>Jalview discovers references for a sequence by generating a set
56 of ID queries from the ID string of each sequence in the alignment. It
57 then tries to query a subset of all the databases it can access in
58 order to match the alignment sequence to any records retrieved from
59 the database. If a match is found, then the sequence is annotated with
60 that database's reference, and any cross-references that its records
63 <strong>The Sequence Identification Process</strong><br> The
64 method of accession id discovery is derived from the method which
65 earlier Jalview versions used for UniProt sequence feature retrieval,
66 and was originally restricted to the identification of valid UniProt
67 accessions.<br> Essentially, Jalview will try to retrieve records
68 from a subset of the databases accessible by the <a
69 href="../features/seqfetch.html">sequence fetcher</a> using each
70 sequence's ID string (or each string in the ID separated by the
73 <p>If a record (or set of records) is retrieved by any query derived
74 from the ID string of a sequence, then the sequence is aligned to the
75 ones retrieved to determine the correct start and end residue
76 positions (which are displayed when the 'Show Full Sequence ID'
77 option). This is important for the correct display of the location of
78 any features associated with that database.</p>
79 <p>If the alignment reveals differences between the sequence in the
80 alignment and the one in the record, then Jalview will assume that the
81 aligned sequence is not the one in the retrieved record.</p>
83 In some cases, the ID used to retrieve records may be out of date and
84 a dialog box will be opened indicating that a 100% match between the
85 sequence and the record was identified, but the sequence name is
86 different. In this case, the can be manually changed (by right
87 clicking on the sequence ID and selecting <strong>Sequence→Edit
90 <li><em>Note</em><br> Please remember to save your alignment
91 if either the start/end numbering, or the sequence IDs were updated
92 during the ID retrieval process.</li>