[Bioperl-l] blast question

[Smithies, Russell]

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<mailto: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<mailto: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> [mailto: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<mailto: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<mailto: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<mailto: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<mailto: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 _______________________________________________
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> 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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