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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: Monday 5th November 2012 21:04:07 UTC (over 3 years ago)
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:[email protected]]
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
> wrote:
That in fact is the recommendation (migrate to BLAST+).

chris

On Nov 4, 2012, at 3:00 PM, "Smithies, Russell"
>
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:
[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
_______________________________________________
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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

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
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