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Gmane
From: Smithies, Russell <Russell.Smithies <at> agresearch.co.nz>
Subject: Re: blast question
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Sunday 4th November 2012 21:00:37 UTC (over 3 years ago)
What version of blast are you using?
There have been quite a few bug fixes and I suspect any responses from NCBI
will suggest upgrading to the current version of blast+


--Russell

-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of shalabh sharma
Sent: Saturday, 3 November 2012 3:50 a.m.
To: Fields, Christopher J
Cc: bioperl-l; [email protected]
Subject: Re: [Bioperl-l] blast question

I know, i am really worried about my past analysis now.
Thanks a lot for cc'ing this mail Chris.

-Shalabh

On Thu, Nov 1, 2012 at 5:41 PM, Fields, Christopher J
 wrote:

> 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 
> 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 
> > _______________________________________________
> > Bioperl-l mailing list
> > [email protected]
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences University of Georgia Athens, GA 30602-3636
_______________________________________________
Bioperl-l mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/bioperl-l

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CD: 3ms