[Bioperl-l] bioperl support for running blast locally

[Peng Yu]

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