[Bioperl-l] bl2seq for many

Chris Fields cjfields at uiuc.edu
Fri May 16 11:24:31 EDT 2008


Not sure what you mean here, as bl2seq uses two sequences.  From the  
bl2seq doc:
"Bl2seq performs a comparison between two sequences using either the  
blastn or blastp algorithm. Both sequences must be either nucleotides  
or proteins. The options may be obtained by executing 'bl2seq -'."
If you mean running multiple rounds of bl2seq with varying sequences,  
the boilerplate demo in the Bio::Tools::Run::StandAloneBlast synopsis  
could be modified to do what you want:

my $factory = Bio::Tools::Run::StandAloneBlast->new(-program =>  
'blastp');
# grab two sequences at a time (loop?) and run bl2seq
my $bl2seq_report = $factory->bl2seq($seq1, $seq2);

Does this answer your question?

-chris

On May 16, 2008, at 9:32 AM, Aparna Pallavajjala wrote:

> Hi,
>
> I would like to know if anyone tried to do bl2seq for multiple  
> sequences at a time?
>
> Please let me know how.
>
> Thx,
> Aparna
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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