[BiO BB] clustering short sequences

[Narcis Fernandez-Fuentes]

I wrote my own greedy algorithm. But I am going to use the program you 
used and compare the resutls.

Narcis


Samantha Fox wrote:
> I had a similar problem, but with dna sequences .. I finally used align0 
> of fasta package .. what was the get-around you used ?
> align0 worked pretty well for me, as I did not want to penalize end-gaps.
> 
> Sam
> 
> On 11/17/05, *Narcis Fernandez-Fuentes* <narcis at fiserlab.org 
> <mailto:narcis at fiserlab.org>> wrote:
> 
> 
>     Hi all,
> 
>       Does anybody knows a program to sequentially cluster short protein
>     fragments, between 8 to 14 residues long? I tried cd-hit, it works find
>     in the range of 12 to 14 but below it crash. Any suggestion?
> 
>     Thanks!
> 
>     Narcis
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-- 
Narcis Fernandez-Fuentes, phD
Seaver Center for Bioinformatics
Albert Einstein College of Medicine
1300 Morris Park Ave, Bronx, NY 10461, USA
phone: (718)430-3233    fax: (718) 430-8565
mailto:narcis at fiserlab.org  (http://www.fiserlab.org)