[Bioperl-l] bioperl support for running blast locally

[Peng Yu]

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