Can anyone suggest useful R resources (either full programs or pieces of code) to do comparative genomics such as genome visualization, alignments, ortholog detection, phylogeny construction, etc.? ****************** soranim at pharmacy.ucsf.edu Marco Sorani Program in Biological & Medical Informatics University of California, San Francisco

On Jun 15, 2005, at 12:35 PM, Sorani, Marco wrote: > Can anyone suggest useful R resources (either full programs or pieces > of code) to do comparative genomics such as genome visualization, > alignments, ortholog detection, phylogeny construction, etc.? > You may want to look at biomaRt. It allows mapping genes/affymetrix arrays from one organism to another via the Ensembl mart database. I know you asked about R, but have you looked at bioperl? The tools for doing genome-based work are fairly well-developed, though the learning curve is steep. I'm showing my bias here, so you will probably benefit from hearing from others. Sean