[BioC] Fwd: Re: cross species CGH Nimblegene arrays

Robert Gentleman rgentlem at fhcrc.org
Thu May 8 00:54:12 CEST 2008

Sean Davis wrote:
> On Wed, May 7, 2008 at 6:29 PM, mb23 <mb23 at net.hr> wrote:
>>  I mean that we wanted to compare CNV between 2 individuals of the same species by putting it on the
>>  Danio (zebrafish) CGH array. This fish is according to our previous data quite syntenic to Danio,
>>  although the year 100 millions years apart.
>>  So I am asking if anybody did something like Human to Chimp hybe, or any other on CGH?
>>  thank you!
> If you have an assembled genome (or parts of one), then it is pretty
> simple to use a program like Blat, gmap, etc. to realign the sequences
> on the array to the novel genome.  Then, you can proceed as if the
> array contained sequences for the new species.

   Or even Biostrings for the mapping...:-)
> Hope that helps.
> Sean
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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