I am searching short peptide sequences using blast+ and retrieving the data as an XML table. However, when a 9 amino acid stretch matches within a 10 amino acid query, the program returns a 90% match but only reports the 9 matches and not the terminal mismatch. Anyone know how to force it to report all 10 amino acids?
For example. BLASTing ETTTGVHNLY returns 2 sequences that match 90% ETT(I)GVHNLY and ETTTGVHNL(F). But, the report doesn't have the terminal F in the second. I had to manually research that particular sequence and translate the nt code to find out that the Y was now a F.