[Bioperl-l] blast question

[Fields, Christopher J]

That's a scary error, but the best place to submit this would be the BLAST help list at NCBI (cc'd)

chris

On Nov 1, 2012, at 2:36 PM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> Hi All,
>          First of all i am really very sorry for posting blast question in
> this forum, I am not sure if this is the right place.
> I will really appreciate if anyone can guide me to the right direction.
> 
> I am using blastall to get a top hit from a database so i am using -v 1 -b
> 1 (i hope this is right).
> But the strange part is that i am getting wrong results.
> 
> for example: if i use -v 1 -b 1 then for one of the hit i am getting this:
> 
> 
> Sequences producing significant alignments:                      (bits)
> Value
> 
> fig|6666666.11092.peg.487 Thiol:disulfide oxidoreductase TlpA          38
> 4e-04
> 
> 
> If i use -v 3 -b 3 then i am getting this for the same query:
> 
> Sequences producing significant alignments:                      (bits)
> Value
> 
> fig|6666666.11092.peg.1134 COG3118: Thioredoxin domain-containin...   570
> e-167
> fig|6666666.11092.peg.487 Thiol:disulfide oxidoreductase TlpA          38
> 9e-07
> fig|6666666.11092.peg.1133 Exodeoxyribonuclease III (EC 3.1.11.2...    18
> 1.0
> 
> As you can see the top hit in the first case is totally wrong.
> 
> I would really appreciate if someone can help me out, or direct to in the
> right direction.
> 
> Thanks
> Shalabh
> 
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
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