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The Human Genome Sequencing Center is
working to sequence and annotate the genome of the
cow, Bos taurus.
The cow project includes BAC and
Whole Genome Shotgun (WGS) libraries.
Three genome assemblies have been produced.
A final draft assembly that incorporates
both the BAC and WGS data has been
released.
The source of the BAC library DNA was Hereford bull L1 Domino 99375,
registration number 41170496. Dr. Michael MacNeil's laboratory, USDA-ARS,
Miles City, MT provided the blood. The DNA for the whole genome shotgun
sequences was provided by Dr. Timothy Smith's laboratory,
U.S. Meat Animal Research Center,
Clay Center, NE from white blood cells from L1 Dominette
01449, American Hereford Association registration number 42190680 (a
daughter of L1 Domino 99375). A skin cell fibroblast
cell line from the same animal is available from Dr. Carol Chitko-McKown's
laboratory, although there is no sequence from that cell line.
Funding for this project has been provided by:
the National Human Genome Research Institute (NHGRI U54
HG003273), which is part of the National Institutes
of Health (NIH);
the U.S. Department of Agriculture's Agricultural
Research Service and Cooperative State Research,
Education, and Extension Service (USDA ARS
Agreement No. 59-0790-3-196 and CSREES
Agreement No. 2004-35216-14163); the state of Texas;
Genome Canada through
Genome British Columbia,
The Commonwealth Scientific
and Industrial Research Organization of Australia
(CSIRO); Agritech
Investments Ltd., Dairy Insight, Inc. and
AgResearch Ltd., all of New Zealand;
the Kleberg Foundation; and the National, Texas and South Dakota Beef
Check-off Funds.
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Genome Assembly
The final draft assembly (7.1 fold coverage) and the two previous assemblies are available for
download
as contigs or linearized scaffolds. The assemblies are described in more detail in the README files.
BLAST searches
HGSC provides
BLAST searches of the genome assemblies,
either as contigs or as linearized chromosome sequences.
The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads
that did not end up in the genome assembly) can also
be searched by BLAST.
Traces are available from the
NCBI Trace Archive,
which can be searched using NCBI MegaBLAST with a same species or cross species query.
BAC-based Data Resources
BAC sequencing data is available. BAC data produced from individual shotgun libraries
or from deconvoluted pooled BAC arrays are accessioned
as BAC clone assemblies in GenBank. These can be searched using the
Sequencing Project Browser with a query of:
- an Accession number (AC141790 )
- a Clone name (CH224-59E2)
- or a Project name (AMCL)
in the appropriate query box.
Use the BAC Fisher
to find Whole Genome Shotgun reads that overlap
sequencing reads from a clone. This program finds similar
sequences where the matches extend to the end of the query
sequences. BAC-Fisher
is tuned to reject repeat matches without masking repeats in the query.
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