[Bioperl-l] blast question

[shalabh sharma]

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