[Bioclusters] [Fwd: [BiO BB] question on clustering]

J.W. Bizzaro bioclusters@bioinformatics.org
Thu, 05 Aug 2004 19:21:40 -0400

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Subject: [BiO BB] question on clustering
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Date: Fri,  6 Aug 2004 00:16:47 +0100

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,
BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board@bioinformatics.org