[Bioperl-l] All-vs-all BLAST

[Jason Stajich]

They are moved to a different directory
http://doc.bioperl.org/bioperl-run/
see
http://www.bioperl.org/Core/Latest/faq.html#Q6.2

On Tue, 20 Jul 2004, James Wasmuth wrote:

> The documentation for TCoffee and Clustalw are not available through
> docs 1.4. Though I'll stand corrected.
>
> try:
> http://doc.bioperl.org/releases/bioperl-1.0.2/Bio/Tools/Run/Alignment/Clustalw.html
>
> -james
>
> 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
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu