[Bioperl-l] blast question

[Fields, Christopher J]

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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