[BioC] cross species CGH Nimblegene arrays

[Alicia Oshlack]

Hi,

I think they did chimp on a human array in this paper:
http://www.pnas.org/cgi/content/full/103/21/8006

Also, we published some cross-species microarray mRNA work in this paper
and so if you are doing within species comparisons your idea should work
to the extent that you can map the probes:

http://bioinformatics.oxfordjournals.org/cgi/content/full/23/10/1235

Alicia

> Date: Thu, 08 May 2008 00:54:10 +0200
> From: "mb23" <mb23 at net.hr>
> Subject: Re: [BioC] Fwd: Re: cross species CGH Nimblegene arrays
> To: "Sean Davis" <sdavis2 at mail.nih.gov>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <48223312.180.63cc.257890810 at net.hr>
>
> Well the genome of this species is not sequenced, we just have the idea
> about synteny by anchoring
> to the Danio genome the markers that we used for QTL analysis  which
> gave as an idea, that was done
> by Blat. So we do not have any other idea in terms of sequences about
> the genome of the species.
> thanks!
>
> From: "Sean Davis" <sdavis2 at mail.nih.gov>
> To: mb23 at net.hr
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Fwd: Re: cross species CGH Nimblegene arrays
> Date: Wed, 7 May 2008 18:34:56 -0400
>
> ----- Original Message Follows -----
>> 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.
>>
>> Hope that helps.
>> Sean
>
>
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