[BiO BB] Clustering small DNA sequences into groups

[Bossers, Alex]

Have you tried TGICL? No experience wit small sequences but its good to
configure. No machine at hand to test it :(.
http://www.tigr.org/tdb/tgi/software/


Alex

> -----Oorspronkelijk bericht-----
> Van: bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.org
>
[mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.or
g]
> Namens Samantha Fox
> Verzonden: woensdag 10 augustus 2005 6:29
> Aan: mgollery at unr.edu; The general forum at Bioinformatics.Org;
dmb at mrc-
> dunn.cam.ac.uk; operon at cbiot.ufrgs.br; idoerg at burnham.org
> Onderwerp: Re: [BiO BB] Clustering small DNA sequences into groups
> 
> Well, I had thought that there will be some tools to do what I wanted.
> Maybe I will explain a bit more. Say I have these dna sequences
> tataa, tattta, ttaata, taaaaa, tatata, aattaa,ataaa, tctttc, ttcatt,
acttca.
> 
> Now maybe some sort of grouping or clustering.... in this small
> example last 3 fall in one group ... somehow...
> 
> Any clues !
> 
> Samantha
> 
> >
> > On 8/9/05, Martin Gollery <marty.gollery at gmail.com> wrote:
> > > 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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