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How to get blast to report full sequence

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?

blast
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updated by Ram Ram • written by charlestspencer • charlestspencer

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?

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updated by Ram Ram • written by dariober dariober

1 answer

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

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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.

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updated by Ram Ram • written by charlestspencer • charlestspencer

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).

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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