R help - Sep 2003 - Need help with cluster analysis of amino acid sequences

I am just starting to use R and am wanting to use the cluster algorithm for
analyzing sequences of amino acids for similarities.  The input will be
lists of short sequences of 8-15 amino acids.

Let me give you a feel for the sort of data I am interested in.

 Amino acids can be classified by a number of different parameters: e.g.,
charge and hydrophobicity.  Each of these qualities could be described by a
numerical assignment: charge (perhaps as either 0 or 1), and hydrophobicity
(perhaps as a continuum from 0 to 1).  The point of the analysis is to
cluster those sequences that have similar properties at different positions
along the sequence.

My question is: is there a user group of biologists that may be able to
provide tips about how to proceed, or perhaps who already have developed
algorithms that can be applied/modified to the sort of analysis I need?

Or does anyone have suggestions of other on-line resources that might be
helpful?

Thanks, Peter

Peter Hornbeck
Magnolia, MA
01930
(978) 5264867

The bioconductor project [1] might be of interest to you, and its mailing list 
[2] is probably more appropriate for your question.

[1] http://www.bioconductor.org
[2] https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

HTH,

Deepayan

On Sunday 07 September 2003 12:28, Peter Hornbeck wrote:
> I am just starting to use R and am wanting to use the cluster algorithm for
> analyzing sequences of amino acids for similarities.  The input will be
> lists of short sequences of 8-15 amino acids.
>
> Let me give you a feel for the sort of data I am interested in.
>
>  Amino acids can be classified by a number of different parameters: e.g.,
> charge and hydrophobicity.  Each of these qualities could be described by a
> numerical assignment: charge (perhaps as either 0 or 1), and hydrophobicity
> (perhaps as a continuum from 0 to 1).  The point of the analysis is to
> cluster those sequences that have similar properties at different positions
> along the sequence.
>
> My question is: is there a user group of biologists that may be able to
> provide tips about how to proceed, or perhaps who already have developed
> algorithms that can be applied/modified to the sort of analysis I need?
>
> Or does anyone have suggestions of other on-line resources that might be
> helpful?
>
> Thanks, Peter
>
> Peter Hornbeck
> Magnolia, MA
> 01930
> (978) 5264867
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help