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23 <title>PDB Sequence Fetcher</title>
27 <strong>PDB Sequence Fetcher</strong>
28 <p>From Jalview 2.x.x a speciliased 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 cross-reference other bioinformatics websites before retrieving
33 a 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>
37 The PDB Sequence Fetcher interface can be opened by selecting <strong>PDB</strong>
38 as the choice database from the <strong>'Select Database
39 Retrieval Source'</strong> interface of <a href="seqfetch.html">Sequence
43 <img src="pdbseqfetcher.png" align="left"
44 alt="PDB sequence fetcher (introduced in Jalview 2.x.x)">
48 <strong>Searching the PDB Database</strong><br> Once the
49 interface is opened, typing in the search text box will execute a live
50 query to the PDB database and display the results on-the-fly as seen
51 in the screen-shot above. Use the drop-down menu to select a specific
52 field to search by in the PDB database, the default option is <strong>'ALL'</strong>.
55 <br>Wild card searching: The PDB sequence fetcher also provides support for wild card querying of the PDB database.
56 <br>Single character (matches a single character) - ?
57 The search string te?t would match both test and text.
59 <br>Multiple characters (matches zero or more sequential characters) - *
62 tes* - would match test, testing, and tester.
65 You can also use wildcard characters in the middle of a term. For
67 te*t - would match test and text.
68 *est - would match pest and test.
72 <strong>Customising displayed meta-data</strong> <br>To change the
73 displayed meta-data in the search result, click the <strong>'Configure
74 Displayed Columns'</strong> tab, then tick off the options wanted.
76 <p><strong>Importing Sequence</strong><br>
77 After querying the PDB database, to import the found data into Jalview, select the entries you wish to import then click the ok button at the bottom of the interface.</p>
79 <em>The PDB Sequence Fetcher interface was introduced in Jalview