Photo courtesy of Michael MacNeil, USDA|
(NHGRI Press Photos)
The Mar. 2005 Bos taurus draft assembly (Btau_2.0) was obtained from the Baylor College of Medicine Human Genome Sequencing Center.
A genome position can be specified by the accession number of a sequenced mRNA or EST, a scaffold coordinate range, a gene identifier, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the cow genome. See the User's Guide for more information.
||Genome Browser Response:
|chr1||Displays all of chr1|
|scaffold100||Displays all of scaffold100 (on an unmapped genome assembly)|
|chrM:1-2,500||Displays first 2500 bp of the cow mitochondrion genome|
|chrBin0:1,000-11,000||Displays a region of artificial chromosome Bin0|
|chr1:10000+2000||Displays a region of chr 1 that spans 2000 bases, starting with position 10000|
|BM089574||Displays EST with GenBank accession BM089574|
|AF527382||Displays mRNA with GenBank accession AF527382 (ankyrin repeat and SOCS box)|
|PCDHB1||Lists sequences associated with gene symbol PCDHB1 (protocadherin)|
|prion||Lists sequences associated with keyword prion|
|pseudogene mRNA||Lists transcribed pseudogenes, but not cDNAs|
|zinc finger||Lists sequences associated with keywords "zinc finger"|
|McDaneld,T.G.||Lists mRNAs deposited by author T.G. McDaneld|
|Use this last format for author queries. Although GenBank requires the search format McDaneld TG, internally it uses the format McDaneld,T.G..|
The Btau_2.0 release was assembled from whole genome shotgun (WGS) reads using the Atlas genome assembly system. Several WGS libraries, with inserts of 2 - 4 kb and 4 - 6 kb, were used to produce the data. Approximately 23 million reads were assembled, representing about 17.7 Gb of sequence and 6.2x coverage of the (clonable) bovine genome. Highly repeated sequences and BAC clones sequences were omitted from this assembly; these will be placed in a subsequent version of the draft sequence. 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).
For more information about the bosTau2 assembly, see the Baylor Bovine Genome Project web page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The bosTau2 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.