[BiO BB] question on clustering

Robson Francisco de Souza {S} rfsouza at citri.iq.usp.br
Fri Aug 6 20:55:49 EDT 2004

Take a look at TribeMCL. This software can cluster sequences based on a
similarity score matrix, thouch you will probably have to format your
matrix in an appropriate text format.


> Hi all,
> I have a question that concerns my MSc project. I am trying to cluster 30
> CCP-modules (Complement Receptor 1) after having used a novel approach that
> looks at the electrostatic surfaces. I have reached the stage where I have
> obtained a similarity matrix of 30 by 30 filled with positive scores. The
> higher a score the more similar two modules are. For example, if matrix entry
> (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than
> to module 6 due to a higher score. My problem now is to cluster these 30
> modules based on this one similarity matrix. I am not used to have to cluster
> small datasets or in this case a similarity matrix and not having training
> data. I have searched around a lot on Google for programs that could cluster my
> modules using the similarity matrix but so far I have not found anything very
> helpful. Does anyone know of a program (preferably free software) that could
> help me out here, or another way which I could easily implement myself in a
> script, that would be valid? I would really appreciate all replies to this
> message and thank you all already for looking at this and thinking about this.
> Thanks and regards,
> Floris
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