In October 2007, the Human Genome Sequencing Center at Baylor College of Medicine released an updated assembly of their 7.15X mixed assembly (WGS and BAC sequence) of the bovine genome (Btau_4.0). The source of the DNA was a female of the Hereford breed. The NCBI Bos taurus build Btau_4.0 includes the 7.15X WGS Btau_4.0 assembly and a complete mitochondrial genome derived from a Korean native cow. The bovine genome is organized in 29 pairs of autosomes and a pair of sex chromosomes, X and Y.

The NCBI Map Viewer provides graphical displays of features on the bovine genome sequence assembly. Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map), the WGS sequences (the 'Component' map), and the location of genes, STSs, ESTs, and Gnomon predicted gene models. Extensive documentation is provided to describe the resource features and methods used, tutorials, and statistics.

You can find genes or markers of interest by submitting a query against the whole genome, or a chromosome at a time. Results are indicated both graphically, as tick marks on the ideogram, and in a tabular format. The results table includes links to a chromosome graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display includes the Gene, Ab initio (i.e. the Gnomon predicted models), and estBt (i.e. cow ESTs and mRNAs) sequence maps. You can also browse a chromosome by clicking on a chromosome link in the ideogram above. Use the "Maps & Options" window, available on individual chromosome displays, to configure your display.

The NCBI Map Viewer also presents a graphical view of two non-sequence-based maps for Bos taurus. The genetic map from the Meat Animal Research Center (MARC) was kindly provided by Dr. John Keele. Each of the markers on the genetic map has a link to NCBI's UniSTS resource, which provides regular updates of positioning of these markers on sequences available in DDBJ/EMBL/GenBank. It is thus possible to navigate from these markers to information in Gene, GenBank, RefSeq, HomoloGene and UniGene.

The ILTX_2005 radiation hybrid map contains 3,484 ordered markers, including 3,204 markers that are anchored on the human genome. The map was created using a 5000 rad cattle-hamster RH panel, described by Womack et al., 1997. The details of this third-generation whole-genome and comparative maps are described by Everts-van der Wind, et al 2005. The map is a result of collaboration between the University of Illinois at Urbana-Champaign (H. A. Lewin, PI) and Texas A&M University (J. E. Womack, PI), funded by the USDA National Research Initiative.

Please note that other genomes can also be viewed in the NCBI Map Viewer resource. The Map Viewer Home Page provides a current list. Consider also reviewing the resources listed on the Genomic Biology site.

Available Documentation:

• NCBI Handbook: Map Viewer chapter - resource description
• NCBI Handbook: Map Viewer Exercises - tutorials and examples
• Map Viewer Help - details about navigation and customizing your display
• Genome Assembly - description of genome assembly and annotation process
• Gnomon - description of NCBI's Hidden Markov Model (HMM) ab initio prediction program

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