Hello, I'm looking for a package/function which handles visualization of multiple sequence alignments. Does something like this exist in bioconductor? Thanks, Schraga Schwartz Department of Human Molecular Genetics and Biochemistry, Tel Aviv University Medical School, Tel Aviv 69978, Israel. Tel: +972-3-640 6894 email: schragas@post.tau.ac.il [[alternative HTML version deleted]]

"Schraga Schwartz" <schragas at="" post.tau.ac.il=""> writes: > Hello, > > I'm looking for a package/function which handles visualization of multiple > sequence alignments. Does something like this exist in bioconductor? Not exactly sure what you're looking for; here are a couple of suggestions. There's a package seqLogo that displays sequence 'logos' (variable sized nucleotide letters based on weights) that could be used for this. The development version of ShortRead has, thanks to Simon Anders, a function pileup that collates a large number of alignments into a vector of the number of alignments overlapping each location in a reference sequence. This could then be used with standard R graphics packages, e.g., lattice, or exported to a genome browser with, e.g., rtracklayer. I'm not sure about other visualization tools. These would be fun for someone to develop, if they don't exist. Martin > Thanks, > > > > Schraga Schwartz > > Department of Human Molecular Genetics and Biochemistry, > Tel Aviv University Medical School, > Tel Aviv 69978, Israel. > Tel: +972-3-640 6894 > > email: schragas at post.tau.ac.il > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793