[Bioperl-l] bioperl support for running blast locally

[Chris Fields]

According to the SYNPOSIS and the HOWTO, the factory returns a $result object, which I assume is derived from Bio::SearchIO parsing.  For more information on that see that relevant HOWTO, which gives some illustrative examples.

http://www.bioperl.org/wiki/HOWTO:SearchIO

chris

On Jun 6, 2010, at 2:11 PM, Peng Yu wrote:

> I don't see how StandAloneBlastPlus can help extract all the
> information I need. For example, I need to know the starts and the
> ends of the pair of sequences that match (1 and 33, and 1 and 33 in
> the following example). How many gaps and mismatches there are (no
> gaps and no mismatches in the following example)? The strand
> information.
> 
> Would you please let me know if these are possible with
> StandAloneBlastPlus from git?
> 
> $ blastn -query <(echo
> CGCGGGGATGACTCTAAGCATGGTGCAGGCGATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTC)
> -subject <(echo
> ATCGCCTGCACCATGCTTAGAGTCATCCCCGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGG)
>> HWI-EAS11X_10097_4_1_1909_9532.txt
> $ cat HWI-EAS11X_10097_4_1_1909_9532.txt
> BLASTN 2.2.23+
> 
> 
> Query=
> Length=75
> 
> Subject=
> Length=75
> 
> 
> Score = 62.1 bits (33),  Expect = 1e-15
> Identities = 33/33 (100%), Gaps = 0/33 (0%)
> Strand=Plus/Minus
> 
> Query  1   CGCGGGGATGACTCTAAGCATGGTGCAGGCGAT  33
>          |||||||||||||||||||||||||||||||||
> Sbjct  33  CGCGGGGATGACTCTAAGCATGGTGCAGGCGAT  1
> 
> 
> 
> Lambda     K      H
>   1.33    0.621     1.12
> 
> Gapped
> Lambda     K      H
>   1.28    0.460    0.850
> 
> Effective search space used: 4761
> 
> 
> 
> 
> Matrix: blastn matrix 1 -2
> Gap Penalties: Existence: 0, Extension: 0
> 
> 
> On Sat, Jun 5, 2010 at 6:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> StandAloneBlastPlus is the wrapper for BLAST+ (NCBI's C++-based BLAST implementation).  StandAloneBlast is the C-based legacy BLAST (they have different parameters).
>> 
>> For the rest, please see the associated documentation and the HOWTO:
>> 
>> http://www.bioperl.org/wiki/HOWTO:BlastPlus
>> 
>> chris
>> 
>> On Jun 5, 2010, at 6:16 PM, Peng Yu wrote:
>> 
>>> It seems that StandAloneBlastPlus is a higher level wrapper than
>>> BlastPlus. Is it better to use StandAloneBlastPlus?
>>> 
>>> Essentially, what I need is to compare pairs of sequences. Note that I
>>> want to use the bash Process substitution to avoid generating temp
>>> files. Does StandAloneBlastPlus support this? If yes, would you please
>>> how me what command to use?
>>> 
>>> blastn -query <(echo
>>> GTTGAGTCCAGGCATCCCTGCCATCCCTGAGATCGGAAGAGCGTTTCAGCAGGAATGCCGAGACCGATATCGTAT)
>>> -subject <(echo
>>> CAGGGATGGCAGGGATGCCTGGACTCAACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGT)
>>> 
>>> 
>>> On Sat, Jun 5, 2010 at 5:55 PM, Florent Angly <florent.angly at gmail.com> wrote:
>>>> To run BLAST locally, see  bioperl-run  / lib  / Bio  / Tools  / Run  /
>>>> BlastPlus.pm
>>>> Then to parse the results, you can read this:
>>>> http://www.bioperl.org/wiki/HOWTO:SearchIO
>>>> Florent
>>>> 
>>>> On 06/06/2010 07:28 AM, Peng Yu wrote:
>>>>> 
>>>>> There is a module to run blast remotely
>>>>> Module:Bio::Tools::Run::RemoteBlast. But I installed blast locally and
>>>>> I think that it makes more sense for me to run blast locally. Is there
>>>>> a way to let bioperl parse the output from my local command line
>>>>> blast?
>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> Regards,
>>> Peng
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 
> 
> -- 
> Regards,
> Peng
> 
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