Dear Richard, Dotmatcher uses a specified substitution matrix: http://emboss.open-bio.org/wiki/Appdoc:Dotmatcher
Best regards, Stefan 2011/7/27 Richard Friedman <[email protected]>: > 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) > [email protected] > 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 > > > > > > > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
