[Bioperl-l] blast question

Mon Nov 5 21:09:03 UTC 2012

Hi All,
           Thanks for all the suggestion. The problem is fixed by using
latest blast+ .
Thanks
Shalabh

On Mon, Nov 5, 2012 at 4:04 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> If you’re using an older version of blast there was a bug where not all
> results were returned – I think the limit was 10,000 hits?****
>
> Not usually a problem running basic queries but a big problem for
> environmental or metagenomic samples, or when aligning short reads.****
>
> ** **
>
> --Russell****
>
> ** **
>
> *From:* shalabh sharma [mailto:shalabh.sharma7 at gmail.com]
> *Sent:* Tuesday, 6 November 2012 6:04 a.m.
> *To:* Fields, Christopher J
> *Cc:* Smithies, Russell; bioperl-l
>
> *Subject:* Re: [Bioperl-l] blast question****
>
> ** **
>
> Hi All,****
>
>          thanks for all your responses.****
>
> ** **
>
> Currently i am using the old version of blastall 2.2.22.****
>
> ** **
>
> @Peter: I will update my blast and will see if the problem still exist.
> But i can't restrict my blast with e value because i work on environmental
> samples , i have to reduce the size of my blast files as i am only
> interested in the top hit and my data sets are really huge.****
>
> ** **
>
> Thanks****
>
> Shalabh****
>
> ** **
>
> On Sun, Nov 4, 2012 at 5:13 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:****
>
> That in fact is the recommendation (migrate to BLAST+).
>
> chris****
>
>
> On Nov 4, 2012, at 3:00 PM, "Smithies, Russell" <
> Russell.Smithies at agresearch.co.nz> wrote:
>
> > 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: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> > Sent: Saturday, 3 November 2012 3:50 a.m.
> > To: Fields, Christopher J
> > Cc: bioperl-l; blast-help at ncbi.nlm.nih.gov
> > 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 <
> cjfields at illinois.edu
> >> 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 <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
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> 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
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
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>
>
> ****
>
> ** **
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636****
>
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-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636