[Bioperl-l] All-vs-all BLAST

[Peter van Heusden]

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

Peter