Annotation of the bovine (Bos Taurus) genome

[gwilymh]

Hi,

I am very new to bioinformatics, and am presently analyzing exon-capture data using the Bos taurus (cattle) genome. I am trying to work out how to identify SNPs in a series of target genes. Unfortunately, the only annotated Bos taurus genome I have been able to find is the UMD_3.1 version posted on NCBI. I would prefer to work with the Btau_4.0, 4.2 or 6.6 genomes, but these do not appear to be annotated on the UCSC Genome Bioinformatics site (http://hgdownload.cse.ucsc.edu/downloads.html). Does anyone know how or where I can download annotations for these genome assemblies?

[westerman]

Look at the following.

http://tophat.cbcb.umd.edu/igenomes.html