[Bioperl-l] All-vs-all BLAST

Andreas Kahari ak at ebi.ac.uk
Thu Jul 22 06:32:07 EDT 2004

On Thu, Jul 22, 2004 at 11:09:45AM +0100, Peter van Heusden wrote:
> richard sucgang phd wrote:
> >At 10:52 AM -0400 7/20/04, Jason Stajich wrote:
> >
> >>If you want to run blast I don't think you really need Bioperl.
> >
> >
> >I had to wait until someone more knowledgable like Jason said this.
> >The NCBI BLAST package includes a binary called blastclust that 
> >automatically runs the all vs all comparison of a set of sequences and 
> >divides them into clusters (which is the usual reason for running such 
> >a comparison).
> >
> If you're looking to do clustering, however, why not use actual 
> clustering software? For instance, Electric Genetics' (yeah, my 
> empoyer!) provides stackPACK, a clustering toolkit (focussed on ESTs) 
> which is free for academics: http://www.egenetics.com/stackpack.html

Or MCL, which I think Jason has provided some blast-related
input to:


Andreas Kähäri

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