[BiO BB] Clustering small DNA sequences into groups

Martin Gollery marty.gollery at gmail.com
Tue Aug 9 15:24:18 EDT 2005


I believe those sequences are too short for Blastclust. The default
word size is 32.

Marty

On 8/9/05, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br> wrote:
> 
> 
> Hi Samantha,
> 
> BLASTCLUST can group DNA sequences. Maybe you will need to tweak the
> parameters (almost the same for BLAST). You can get it at the NCBI ftp:
> ftp://ftp.ncbi.nih.gov/blast/
> 
> cheers
> Marcos
> 
> 
> 
> On Tue, 09 Aug 2005 14:24:41 -0300, Samantha Fox <bioinfosm at gmail.com>
> wrote:
> 
> > Hi,
> >
> > I have a set of small DNA sequences (about 40) 6-10 bp, and wish to
> > group them into clusters based on sequence.
> >
> > Any suggestions for doing that ?
> >
> > Thanks,
> >
> > Samantha
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> 
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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