BLAST search of short ambiguous sequences?

Aawara Chowdhury via (by aawara from
Mon Aug 11 20:25:56 EST 2008

In <04522ce8-e4bd-48ea-bf69-9178f6fd13ea from>,
 WS <novalidaddress from> wrote:

> Dear experts,
> I would like to search a genomic database for the occurrence of short
> motifs, like eg {Y,S,T} X {K,R}XX {Y,S,T}
> X means any amino acid, lists in {} are 2 or 3 amino acids at a
> specific position.
> Instead of generating all possible combinations and blasting them
> separately, is there a smarter way to do it? I couldn't find any hints
> in the BLAST documentation at NCBI

If you have a few sequences that match this consensus, then you can do a
PHI BLAST search.  I just did this a little while ago, and it worked 
well.  My pattern was about 8 a.a. long.

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