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Seqence alignement iteration - (Jun/07/2010 )

;) I have a short peptide of about 30 amino acids that I would like to BLAST against protein databases, pentapeptide by pentapeptide (or hexapeptide, heptapeptide etc) to look for matching sets (eg, cleavage sites, etc). Other than doing this by hand, is there a BLAST setting for doing this and from which server?

Thanks for any help



If i understand correctly, try
choose protein blast?

-adrian kohsf-