[EMBOSS] dotplots taking similarity into account

[Stefan]

Dear Richard,

Dotmatcher uses a specified substitution matrix:
http://emboss.open-bio.org/wiki/Appdoc:Dotmatcher

Best regards,
Stefan

2011/7/27 Richard Friedman <friedman at cancercenter.columbia.edu>:
> 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,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> 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
> http://cancercenter.columbia.edu/~friedman/
>
> I am a Bayesian. When I see a multiple-choice question on a test and I don't
> know the answer I say "eeney-meaney-miney-moe".
>
> Rose Friedman, Age 14
>
>
>
>
>
>
>
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