How to get blast to report full sequence

Question

[charlestspencer]

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?

[dariober]

Just checking...: Blast performs local alignment, so hits might be truncated if that improves the alignment score. Are you sure you don't want global alignment instead?

Answer 1

[Pierre Lindenbaum]

Do you only want to get the full sequence of the Hit? Extract the Hit ID from the output and get the whole sequence with blastdbcmd

[charlestspencer]

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.

[Pierre Lindenbaum]

That's what I'm saying: retrieve the whole sequence of the hit using blastdbcmd . If could also look for another algorithm (global alignment vs local=blast).