BLAST search of short ambiguous sequences?

WS via (by novalidaddress from
Sat Aug 9 05:40:42 EST 2008

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

Many thanks,


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