Question: How to get blast to report full sequence
0
gravatar for charlestspencer
4.9 years ago by
United States
charlestspencer0 wrote:

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 • 1.8k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by charlestspencer0
1

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?

ADD REPLYlink written 4.9 years ago by dariober10k
0
gravatar for Pierre Lindenbaum
4.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

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

 

ADD COMMENTlink written 4.9 years ago by Pierre Lindenbaum125k

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.

ADD REPLYlink written 4.9 years ago by charlestspencer0

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).

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum125k
0
gravatar for charlestspencer
4.9 years ago by
United States
charlestspencer0 wrote:

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.

ADD COMMENTlink written 4.9 years ago by charlestspencer0
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