[BiO BB] Clustering

[Iddo Friedberg]

Dan Bolser wrote:
> Hi, 
> 
> What packages support clustering of points
> with a with a similarity matrix?

I don't think I quite understand the question, can you elaborate on that?

> 
> How can I derive the similarity of two matrices?
> 

If you mean that you would like to check how "close" two similarity 
matrices (e.g. BLOSUM, PAM) are to each other, then one method is to 
compare the amino-acid pair frequency distributions used to construct 
these matrices. Look to the following paper (fig 4, and the last 
paragraph in the "methods" section) for one example on how to do this, 
although other methods of comparing distributions may be used just as 
effectively:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=11790845&dopt=Abstract

./I




-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo