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  Cow (Bos taurus) Genome Browser Gateway
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  About the Cow Oct. 2007 (bosTau4) assembly (sequences)
Bos Taurus
Photo courtesy of Michael MacNeil, USDA
(NHGRI Press Photos)

The October 2007 Bos Taurus draft assembly (Baylor release Btau_4.0) was produced by the Baylor College of Medicine Human Genome Sequencing Center. For more information about this assembly, see Btau_4.0 in the NCBI Assembly database.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, 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.

Request:   Genome Browser Response:
chr28   Displays all of chromosome 28
chr28:1-1000000   Displays first million bases of chromosome 28
chr28:1000000+2000 Displays a region of chr 28 that spans 2000 bases, starting with position 1000000
BC140604   Displays region of mRNA with GenBank accession number BC140604
EE384456   Displays region of EST with GenBank accession EE384456 on chr X
pseudogene mRNA   Lists transcribed pseudogenes, but not cDNAs
homeobox caudal   Lists mRNAs for caudal homeobox genes
zinc finger   Lists many zinc finger mRNAs
kruppel zinc finger   Lists only kruppel-like zinc fingers
zhang   Lists mRNAs deposited by scientist named Zhang
Moore,S.   Lists mRNAs deposited by co-author S. Moore
Use this last format for author queries. Although GenBank requires the search format Moore S, internally it uses the format Moore,S..

Assembly details

The Btau_4.0 release was produced by the Atlas genome assembly system at Baylor College of Medicine Human Genome Sequencing Center. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 11869 scaffolds (named chrUn.004.*). The mitochondrial sequence (chrM) was obtained from Genbank accession GI:60101824.

The Btau_4.0 assembly (7.1x coverage) was tested against available bovine sequence data sets (EST sequences and finished BAC sequences) for extent of coverage (completeness). When assembled contigs were tested, over 95% of the sequences in these data sets were found to be represented, indicating that the shotgun libraries used to sequence the genome were comprehensive. Of the 1.04 million EST sequences 95.0% were contained in the assembled contigs. Assuming the ESTs are uniformly distributed throughout the genome, the estimated genome size is 2.73 Gb/95% = 2.87 Gb. For detailed information on the sequencing and assembly techniques, see the Readme file that accompanies this release and 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 bosTau4 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.

Genbank Pipeline Details

For the purposes of the Genbank alignment pipeline, this assembly is considered to be: well-ordered.