[Bioperl-l] All-vs-all BLAST

James Wasmuth james.wasmuth at ed.ac.uk
Tue Jul 20 10:57:48 EDT 2004

The documentation for TCoffee and Clustalw are not available through 
docs 1.4. Though I'll stand corrected.



Paulo Almeida wrote:

> 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.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

I like nonsense, it wakes up the brain cells.
		-- Dr. Seuss

Blaxter Nematode Genomics Group  |
School of Biological Sciences    |
Ashworth Laboratories            | tel: +44 131 650 7403
University of Edinburgh          | web: www.nematodes.org
Edinburgh                        |
EH9 3JT                          |
UK                               |	

More information about the Bioperl-l mailing list