3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>PDB Sequence Fetcher</title>
27 <strong>PDB Sequence Fetcher</strong>
28 <p>From Jalview 2.9 a specialised interface was introduced for
29 fast and efficient discovery/retrieval of sequence data from the PDB
30 database. The introduced interface enables live querying of PDB data
31 on-the-fly thereby eliminating the need to memorise database accession
32 or to manually cross-reference other bioinformatics websites before retrieving
33 sequence data in Jalview. The underlying technology is provided by
34 EBI and is based on Apache Solr which is a text based search engine.</p>
36 The PDB Sequence Fetcher interface can be opened by selecting <strong>PDB</strong>
37 as the choice database from the <strong>'Select Database
38 Retrieval Source'</strong> interface of <a href="seqfetch.html">Sequence
42 <img src="pdbseqfetcher.png" align="left"
43 alt="PDB sequence fetcher (introduced in Jalview 2.9)">
46 <p><strong>Searching the PDB Database</strong></p>
47 <p>When the interface is opened, a live query to the PDB database is
48 executed every time a character is typed into the search text box, and
49 a result is displayed on-the-fly as seen in the screenshot above.</p>
51 <p>Use the drop-down menu to select a specific field to search by in the PDB database, the default
52 option is <strong>'ALL'</strong>.</p>
54 <p> Furthermore, the PDB search interface also provides the following functionalities:</p>
56 <li>Retrieving a unique chain for a PDB entry: <br>To
57 retrieve a specific chain for a PDB entry, append the PDB ID with a
58 colon followed by the chain code in the search box. eg: 1xyz:A
61 <li>Querying multiple PDB Id's in one operation:<br>The PDB
62 search interface supports querying of multiple PDB Ids in one
63 operation by separating the list of PDB Ids with a semi-colon i.e:
67 <li>Wild card searching: <br>The PDB sequence fetcher also
68 provides support for wild card querying of the PDB database. <br>Single
69 character (matches a single character) - ? The search string te?t
70 would match both test and text. <br>Multiple characters (matches
71 zero or more sequential characters) - * The wildcard search: tes* -
72 would match test, testing, and tester. You can also use wildcard
73 characters in the middle of a term. For example: te*t - would match
74 test and text. *est - would match pest and test.
78 <strong>Customising displayed meta-data</strong> <br>To change
79 the displayed meta-data in the search result, click the <strong>'Configure
80 Displayed Columns'</strong> tab, then tick off the options wanted.
83 <strong>Importing Sequence</strong><br> After querying the PDB
84 database, to import the found data into Jalview, select the entries
85 you wish to import then click the 'Ok' button at the bottom of the
89 <em>The PDB Sequence Fetcher interface was introduced in Jalview