PDB Sequence Fetcher
From Jalview 2.x.x a speciliased interface was introduced for
fast and efficient discovery/retrieval of sequence data from the PDB
database. The introduced interface enables live querying of PDB data
on-the-fly thereby eliminating the need to memorise database accession
or to cross-reference other bioinformatics websites before retrieving
a sequence data in jalview. The underlying technology is provided by
EBI and is based on Apache Solr which is a text based search engine.
The PDB Sequence Fetcher interface can be opened by selecting PDB
as the choice database from the 'Select Database
Retrieval Source' interface of Sequence
Fetcher.
Searching the PDB Database
Once the interface is opened, typing in the search text box
will execute a live query to the PDB database and display the results
on-the-fly as seen in the screen-shot above. Use the drop-down menu to
select a specific field to search by in the PDB database, the default
option is
'ALL'. Furthermore, the PDB search interface also
provides the following functionalities:
- Retrieving a unique chain for a PDB entry:
To
retrieve a specific chain for a PDB entry, append the PDB ID with a
colon followed by the chain code in the search box. eg: 1xyz:A
- Querying multiple PDB Id's in one operation:
The PDB
search interface supports querying of multiple PDB Ids in one
operation by separating the list of PDB Ids with a semi-colon i.e:
1xyz;2xyz;3xyz
- Wild card searching:
The PDB sequence fetcher also
provides support for wild card querying of the PDB database.
Single
character (matches a single character) - ? The search string te?t
would match both test and text.
Multiple characters (matches
zero or more sequential characters) - * The wildcard search: tes* -
would match test, testing, and tester. You can also use wildcard
characters in the middle of a term. For example: te*t - would match
test and text. *est - would match pest and test.
Customising displayed meta-data
To change
the displayed meta-data in the search result, click the 'Configure
Displayed Columns' tab, then tick off the options wanted.
Importing Sequence
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.
The PDB Sequence Fetcher interface was introduced in Jalview
2.x.x.