There are many alternatives for alignment including blast, blat, gmap,
ssaha, etc.  This could also be done with biostrings.

Sean

On Jul 21, 2010 2:43 PM, "Bazeley, Peter" <Peter.Bazeley@rockets.utoledo.edu>
wrote:

Hi Sean,

For the second option, is there a specific package that you had in mind?
Perhaps the GenomicFeatures package, which can download UCSC tables.


Thanks,
Pete
________________________________
From: seandavi@gmail.com [seandavi@gmail.com] on behalf of Sean Davis [
sdavis2@mail.nih.gov]
Sent: Wednesday, July 21, 2010 7:27 AM
To: Bazeley, Peter
Cc: bioc-devel@stat.math.ethz.ch
Subject: Re: [Bioc-devel] mapping probes/probesets between platforms




On Tue, Jul 20, 2010 at 10:50 PM, Bazeley, Peter <
Peter.Bazeley@rockets.utoledo.edu<mailto:Peter....
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