[Genome] UCSC Cow Genome

[João Fadista]

Dear Brooke,

Thanks for the useful information. 

My problem is that I am trying to analyse CGH microarray data from some chromosomes in the cow and for that I am using some packages in Bioconductor. But these packages only deal with the human genome (in the sense that they have the data frame that I wanted only for human genome). Perhaps I will put the location of the centromeres in the middle of the chromosomes just to see what I get. Do you know when is the next version of the cow assembly be ready? And do you know if it will have the locations of the centromeres?


Best regards

João Fadista
Ph.d. student


UNIVERSITY OF AARHUS
Faculty of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
Blichers Allé 20, P.O. BOX 50
DK-8830 Tjele

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E-mail:  Joao.Fadista at agrsci.dk
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-----Original Message-----
From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] 
Sent: Thursday, January 25, 2007 8:34 PM
To: João Fadista
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] UCSC Cow Genome

Hello João,

The latest UCSC cow assembly is bosTau2, from March 2005.  It has not been completely assembled into chromosomes yet -- much of the assembly is still in scaffolds.  Here is the information about the assembly from the bosTau2 Genome Browser Gateway page:

"The assembly contains chromosomes 1-29, X, M, and Bin0, as well as
98058 scaffolds. Bin0 is an artificial chromosome consisting of contigs of 3 or fewer reads that were not incorporated into scaffolds. Baylor Chr30 is labeled chrX in the UCSC Genome Browser. Baylor artificial chromosome ChrUn was split into scaffolds for display in the browser. 
chrM was obtained from NCBI (gi=12800)."

Because the bosTau2 sequence has not been fully assembled into chromosomes, the locations of the centromeres are not available.

However, you can get a list of chromosomes and their sizes by going to the bosTau2 Genome Browser Gateway page (hit the "Genomes" link at the top of the Genome Browser page and select Cow, March 2005, then just scroll down the page) and hitting the "sequences" link.  The link is right after the words "About the Cow Mar. 2005 (bosTau2) assembly". 
This will give you a list of the chromosomes and scaffolds and their sizes.

I hope this information helps.  Please let us know if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


João Fadista wrote:
> Dear all,
>  
> I would like to know if it is possible to have a dataset that contains basic chromosomal information for the latest UCSC Cow Genome Assembly.
> This dataset should be a data frame with 3 variables (Chromosomal index, Length of each chromosome and the Location of the centromere on the chromosome).
>  
>  
> 
> Med venlig hilsen / Regards
> 
> João Fadista
> Ph.d. studerende / Ph.d. student
> 
> 
>  	
>  	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
> Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences	
> Forskningscenter Foulum / Research Centre Foulum	
> Genetik og Bioteknologi / Dept. of Genetics and Biotechnology	
> Blichers Allé 20, P.O. BOX 50	
> DK-8830 Tjele	
>  	
> Tel:	 +45 8999 1900	
> Direct:	 +45 8999 1900	
> Mobile:	 +45 	
> E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> 	
> Web:	 www.agrsci.dk <http://www.agrsci.dk/> 	
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