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.
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.
PROBLEM SOLVED, see below
Khader you're my man :D
The answer to my question is - PROSITE (link)
Prosite offers the opportunity to handle special patterns (Prosite pattern: http://ca.expasy.org/tools/scanprosite/scanprosite-doc.html#pattern_syntax).
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:
(keep in mind to use the input field 'MOTIF scan' at the left, not 'sequence scan' at the right
BTW. This was my first post at this forum and I'm really surprised about the fast and good qualitative answers :) Thanks a lot!