[Bioperl-l] bioperl support for running blast locally

[Chris Fields]

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
> 
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