[Bioperl-l] All-vs-all BLAST

[Paulo Almeida]

Hi,

You want to compare all the possible pairs of sequences in the set? If 
that is it, you can try putting all the sequences in an array, blast the 
first against all the others, shift it out of the array and then repeat 
the process until the array is empty. If it's a multiple alignment you 
want, you could probably use Bio::Tools::Run::Alignment::Clustalw 
<http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/Alignment/Clustalw.html> 
(I was going to link to the webpage, but that link is broken in the 
Bioperl webpage).

-Paulo

Peter J Stogios wrote:

> Hello,
>
> I'm looking for a script to do an all-vs-all BLAST comparison of a set 
> of sequences.