How do I blast against a specific portion of the nr database?

Question

[phoenixmx]

I would like to blast my sequences against the swissprot database, using local blast. For the purpose of downstream applications, I would like to do this using the copy of the swissprot database from the NCBI's ftp site, not the version from swissprot's own website.

The NCBI version comes as tiny .msk and .pal files, accompanied with this message:

Certain databases are subsets of a larger parental database. For those databases, alias and mask files, rather than actual databases, are provided. The mask file needs the parent database to function properly. The parent databases should be generated on the same day as the mask file. For example, to use swissprot pre-formatted database, swissprot.tar.gz, one will need to get the nr.tar.gz with the same date stamp.

I have both the nr database and swissprot files, with matching date stamps, downloaded and extracted. How do I now blast against the swissprot database? If I try to blast against swissprot as if it were a normal database, it tells me it cannot find 'swissprot.pin'. I have also gone through the help files from my blast executable (blastall 2.2.18) and see no parameters for mask or alias files.

[Pierre Lindenbaum]

cross posted: http://seqanswers.com/forums/showthread.php?t=43245

Answer 1

[Carlos Borroto]

It sounds like you need a newer version of BLAST. I just confirmed I can use the .msk and .pal files for swissprot with 'Protein-Protein BLAST 2.2.28+'.

[phoenixmx]

That might indeed be the case, thank you. The blast installation I have access to on the server I'm using is rather old.

Would you mind please explaining exactly what the correct way to use those files would be? Do I just list set the -database parameter to swissprot, or set the database to nr and include extra parameters pointing to the mask or alis files?

Not having done this before, I don't know what the correct approach is.

EDIT: I've got the most recent BLAST+ executable on the server now, and it works just fine if you set -db as swissprot and let it figure things out itself.