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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 infrastructure 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 accessed from <b>"File →Fetch Sequence(s) →Select Database →PDB"</b> click the ok button after selecting PDB from the 'Select Database
37 Retrieval Source' interface.
40 <img src="pdbseqfetcher.png" align="left"
41 alt="PDB sequence fetcher (introduced in Jalview 2.9)">
44 <p><strong>Searching the PDB Database</strong></p>
45 <p>When the interface is opened, a live query to the PDB database is
46 executed every time a character is typed into the search text box, and
47 a result is displayed on-the-fly as seen in the screenshot above.</p>
49 <p>Use the drop-down menu to select a specific field to search by in the PDB database, the default
52 <p> Furthermore, the PDB search interface also provides the following functionalities:</p>
54 <li>Retrieving a unique chain for a PDB entry: <br>To
55 retrieve a specific chain for a PDB entry, append the PDB ID with a
56 colon followed by the chain code in the search box. eg: 1xyz:A
59 <li>Querying multiple PDB Id's in one operation:<br>The PDB
60 search interface supports querying of multiple PDB Ids in one
61 operation by separating the list of PDB Ids with a semi-colon i.e:
65 <li>Wild card searching: <br>The PDB sequence fetcher also
66 provides support for wild card querying of the PDB database. <br>Single
67 character (matches a single character) - ? The search string te?t
68 would match both test and text. <br>Multiple characters (matches
69 zero or more sequential characters) - * The wildcard search: tes* -
70 would match test, testing, and tester. You can also use wildcard
71 characters in the middle of a term. For example: te*t - would match
72 test and text. *est - would match pest and test.
76 <strong>Customising displayed meta-data</strong> <br>To change
77 the displayed meta-data in the search result, click the 'Configure
78 Displayed Columns' tab, then tick off the options wanted.
81 <strong>Importing Sequence</strong><br> After querying the PDB
82 database, to import the found data into Jalview, select the entries
83 you wish to import then click the 'Ok' button at the bottom of the
87 <em>The PDB Sequence Fetcher interface was introduced in Jalview