[BioC] comparative genomics

Sean Davis sdavis2 at mail.nih.gov
Wed Jun 15 19:27:10 CEST 2005

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.


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