July 2006: NCBI released an update for the rat genome that includes re-annotation of the reference genome assembly and addition of an alternate genome assembly. The reference assembly, representing the BN/SsNHsdMCW genome, is based on RGSC v3.4 'November 2004 update' generated by the Human Genome Sequencing Center at the Baylor College of Medicine as a component of the Rat Genome Sequencing Consortium. The alternate assembly, representing a mixture of the Brown Norway and Sprague-Dawley genomes, is based on Celera Genomics' January 2003 whole genome shotgun (WGS) assembly.

The NCBI Map Viewer provides graphical displays of several types of maps, including sequence maps, two genetic maps, and a radiation hybrid map. Map features that can be seen on the sequence map include NCBI contigs (the 'Contig' map), the WGS sequences (the 'Component' map), and the location of genes, STSs, ESTs, and gene models predicted by Gnomon. By default, data and annotations from the reference assembly is shown. Please see the instructions on how to view data from the alternate assembly. Documentation is provided below 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 one chromosome at a time. Results are indicated both graphically, as tick marks on the chromosomes, or 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 gene models), and Rn RNA (i.e. rat ESTs and mRNAs) sequence maps. Use the "Maps & Options" window to configure each display.

A current list of other genomes viewable in the NCBI Map Viewer is provided on the Map Viewer home page. Also consider 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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