In February 2008, the Wellcome Trust Sanger Institute released a partial BAC-based assembly of the porcine genome (Sscrofa5). It includes assemblies for chromosomes 1, 4, 5, 7, 11, 13, 14, 15, 17 and X. The source of the DNA was a female of the Duroc breed. The NCBI Sus scrofa build 1.1 includes the Sscrofa5 assembly and a complete mitochondrial genome derived from a Landrace pig. The porcine genome is organized in 18 pairs of autosomes and a pair of sex chromosomes, X and Y.

The NCBI Map Viewer provides graphical displays of features on the porcine genome sequence assembly. Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map), the BAC 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 rnaSsc (i.e. pig 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 the MARC linkage map for Sus scrofa. 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.

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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