[Bioperl-l] Fwd: megablast using bioperl

[Mark A. Jensen]

Xiujing--
If you choose to use blast+, this is pretty easily done with
Bio::Tools::Run::StandAloneBlastPlus :

 use Bio::Tools::Run::StandAloneBlastPlus;
 $ENV{BLASTPLUSDIR} = "/path/to/blast+/bin";
 
 $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
    -db_name => '/path/to/blastdb/mydb'
);
 
 $result = $fac->blastn( -query => 'myqueryseqs.fas' );

 while ($hit = $result->next_hit) {
  # process hits
 }

Here, blastn is used, because in blast+, megablast is the default
algorithm. --to specify others, you set the -task parameter: e.g., 
legacy blastn would be
 
 $result = $fac->blastn( -query =. 'myqueryseqs.fas',
                                     -task => 'blastn' );

For much more information, please look at 
http://bioperl.org/wiki/HOWTO:SearchIO
and
http://bioperl.org/wiki/HOWTO:BlastPlus

Many questions you might have will be answered in those pages.
MAJ




----- Original Message ----- 
From: "Jason Stajich" <jason at bioperl.org>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Cc: <xiujingg at yahoo.com>
Sent: Monday, February 01, 2010 2:48 PM
Subject: [Bioperl-l] Fwd: megablast using bioperl


> Xiujing -
> Your message is best asked on the mailing list.
> 
> Begin forwarded message:
> 
>> From: Xiujing Gu <xiujingg at yahoo.com>
>> Date: February 1, 2010 7:58:55 AM PST
>> To: jason at bioperl.org
>> Subject: megablast using bioperl
>>
>> Hello Jason:
>>
>> After numerous googling, I found you might be the only person who  
>> knows about this subject. Would you so kindly show me an example of  
>> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
>>
>> Thanks a lot!
>>
>> Best regards,
>> Xiujing
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