In September 2007, the Broad Institute released the second version of a 6.8X WGS assembly of the domestic horse genome - EquCab2. The source of the DNA was a female Thoroughbred horse named "Twilight" from Cornell University in Ithaca, New York. The NCBI Equus caballus build 2.1 (Eca2.1) includes the WGS assembly and a complete mitochondrial genome, derived from a different horse. The domestic horse genome consists of 31 pairs of autosomes and a pair of sex chromosomes, X and Y.

The NCBI Map Viewer provides graphical displays of features on the horse 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. Available Documentation provides tutorials, statistics, and information about resource features and methods used.

You can find markers of interest by submitting a query against the whole genome, or one chromosome at a time. The results are indicated both graphically, as tick marks on the chromosome, or in a tabular format. Alternatively, you can 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 a whole genome radiation hybrid map for Equus caballus. The map includes 3816 markers of which 1917 are on maximum likelihood (MLE-)consensus (also known as framework) maps, 1311 are placed at centiRay positions in relation to the MLE-consensus maps, and 588 are assigned to bins spanned by two or more consecutive MLE-consensus markers. More information on this map is available here.

Please note that other genomes can also be viewed in the NCBI Map Viewer resource. The Map Viewer Home Page provides a current list of available genomes. 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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