[BiO BB] Clustering small DNA sequences into groups

[Samantha Fox]

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
>