[BioC] comparative genomics

[Sean Davis]

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