[BioC] Fwd: Re: cross species CGH Nimblegene arrays
mb23 at net.hr
Thu May 8 00:54:10 CEST 2008
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.
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.
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