Hi everybody! I do not have much experience in the area of CGH, so I decided to ask everybody for an opinion and experience with CGH.I would like to ask if anybody has an experience with cross species CGH Nimblegene arrays. Does this works well, if the data make any sense or all what u get is just a lot of noise? thank you very much! Marti -- HP pisac uz Iskon.DUO pakete- odaberite paket Obitelj, Surf ili Obitelj+ i dobivate visenamjenski pisac za samo 1 kn! Vise o paketima saznajte na http://www.iskon.hr ili na 0800 1000

On Wed, May 7, 2008 at 6:09 PM, mb23 <mb23 at="" net.hr=""> wrote: > Hi everybody! > I do not have much experience in the area of CGH, so I decided to ask everybody for an opinion and > experience with CGH.I would like to ask if anybody has an experience with cross species CGH > Nimblegene arrays. Does this works well, if the data make any sense or all what u get is just a lot > of noise? Hello, Marti. What exactly do you mean by cross-species CGH Nimblegen arrays? A little more detail here might be helpful in getting a useful answer. Sean

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 > > > -- > HP pisac uz Iskon.DUO pakete- odaberite paket Obitelj, Surf ili Obitelj+ > i dobivate visenamjenski pisac za samo 1 kn! > Vise o paketima saznajte na http://www.iskon.hr ili na 0800 1000 >