Hi there =)
Today I was asked if there is a possibility to BLAST (blastp) for a specific amino acid MOTIF spanning seven amino acids. However this MOTIF is 'dynamic' at 3 points: position 2 in the motif can be either I,L or V; position 5 can be any amino acid (symbolized with n in MOTIF); position 6 and/or 7 must be D.
MOTIF: Q[I,L,V]DGnDD
Is there a possibility to do some regular expressions to BLAST or is there a special option in BLASTP?
...uuh I have no clue and couldn't give the answer...
May be you got a idea how to BLAST this MOTIF.
Thanks
PROBLEM SOLVED, see below
Khader your my man :D
The answer to my question is - PROSITE (link)
Prosite (link) offers the opportunity to handle special patterns (Prosite pattern: link).
However, having a short look at pattern, it does not support the option to do the job for position 6/7 where minimum one of this positions have to be a D. But solving this problem is trivial, I will just write three 'pattern' MOTIFs:
Q-[ILV]-D-G-x-D-D
Q-[ILV]-D-G-x-x-D
Q-[ILV]-D-G-x-D-x
(keep in mind to use the input field 'MOTIF scan' at the left, not 'sequence scan ...
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