[EMBOSS] dotplots taking similarity into account

Richard Friedman friedman at cancercenter.columbia.edu
Wed Jul 27 16:31:01 UTC 2011

Dear Emboss list,

	Is there a way to get dotplots that take similarity according to a  
similarity matrix,
rather than strict  identity into account? As far as I can see, dottup  
is based on identity.
Is there a way that we can dotplots based on a similarity matrix  
similar to dotplot in GCG?
I know that it may be tiresome that I use GCG as a standard, but it is  
what I know and
it is serving as a point of departure while I am learning Emboss and  
redoing the GCG
portion of my course in Emboss. I am enjoying learning about the ways  
in which Emboss
offers improved functionality in the process as well.

Thanks and best wishes,
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu

I am a Bayesian. When I see a multiple-choice question on a test and I  
know the answer I say "eeney-meaney-miney-moe".

Rose Friedman, Age 14

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