MATLAB: How to pass multiple database files to BLASTLOCAL in the Bioinformatics Toolbox 7.8 (R2009a)

Bioinformatics Toolboxblastlocaldatabasefilesmultiple

My BLAST Database is contained in four separate files. How do I input all four files to BLASTLOCAL?

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The files corresponding to the database should begin with a database name and differ only in their extension. i.e.: nr.00.pin, nr.01.pin, nr.02.pin, nr.03.pin

To use all required files in the blast query, pass the name of the database to the BLASTLOCAL command. For example:

results = blastlocal('inputquery', 'myquery.fa', 'database', 'nr', 'program', 'blastx')

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MATLAB: How to limit the BLASTLOCAL query to a subset of the database in Bioinformatics Toolbox 7.8 (R2009a)

The standalone version of Blast is meant to be used on customized database. So one option is to create your own database that represents a filtered version of the NR database. Please see the documentation for FORMATDB, which is available from NCBI.

The attached example shows how you can create your own database in MATLAB. The attached example, 'createDatabaseExample.m' queries Entrez for all the GI-numbers associated with mus musculus and creates a listing of these GI numbers. Then, a restricted database is created.

Another option is to keep the NR database as is, and simply use the '-l' option from BLASTLOCAL. You would still need to use the first part of the attached example to create the file 'mouse.gi'. But then, instead of calling FORMATDB, you could go directly to BLASTLOCAL as follows:

results = blastlocal('inputquery', 'myquery.fa','database', 'nr','program',  'blastp','blastargs', '-l mouse.gi')

(Note that the file mouse.gi.in could also be used, but this is an ASCII file, and the binary mouse.gi would give more efficient file I/O.)

MATLAB: How to change the number of Blast sequence hits returned by BLASTLOCAL in the Bioinformatics Toolbox 7.8 (R2009a)

When calling BLASTALL directly, the '-b' option allows a user to change this value. Typing 'blastall -' at the DOS command prompt (or in MATLAB, '!blastall -') displays usage of the '-b' option. To pass the -b option from BLASTLOCAL append the following parameter/value pair to the BLASTLOCAL call:

blastlocal(...,'blastargs', '-b 10')

if you also want to restrict your query to mouse GI-numbers, the syntax would look like:

blastlocal(...,'blastargs', '-b 10 -l mouse.gi')

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MATLAB: How to limit the BLASTLOCAL query to a subset of the database in Bioinformatics Toolbox 7.8 (R2009a)

MATLAB: How to change the number of Blast sequence hits returned by BLASTLOCAL in the Bioinformatics Toolbox 7.8 (R2009a)

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