Fwd: Re: cross species CGH Nimblegene arrays

0

Entering edit mode

mb23 ▴ 30

@mb23-2787

Last seen 10.2 years ago

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! 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

CGH CGH • 1.1k views

ADD COMMENT • link updated 16.5 years ago by Sean Davis 21k • written 16.5 years ago by mb23 ▴ 30

0

Entering edit mode

Sean Davis 21k

@sean-davis-490

Last seen 12 weeks ago

United States

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

ADD COMMENT • link 16.5 years ago Sean Davis 21k

0

Entering edit mode

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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 206-667-7700 rgentlem at fhcrc.org

ADD REPLY • link 16.5 years ago rgentleman ★ 5.5k

Login before adding your answer.