How To Properly Run Blat Protein Against Protein Database

Question

[arnauvich]

Hi,

I would like to know how to improve BLAT searching for protein matching (matching proteins against proteins databases). Which parameters should be taken into account?

Thanks.

Answer 1

[Michael]

Please refer to the documentation: http://genome.ucsc.edu/goldenPath/help/blatSpec.html excerpt:

options:
 -t=type     Database type.  Type is one of:
                 dna - DNA sequence
                 prot - protein sequence
                 dnax - DNA sequence translated in six frames to protein
               The default is dna
 -q=type     Query type.  Type is one of:
                 dna - DNA sequence
                 rna - RNA sequence
                 prot - protein sequence
                 dnax - DNA sequence translated in six frames to protein
                 rnax - DNA sequence translated in three frames to protein

[arnauvich]

Thanks, I was looking for some advice for optimize the search in a standalone version, which parameters are useful for finding and equilibrium between accuracy and time consuming.

Thanks anyway.

[Michael]

That might be more about the tradeoff between BLAT and BLAST which is more sensitive for distant homologues.