In August 2006, the Human Genome Sequencing Center at Baylor College of Medicine released an ~8X mixed assembly (WGS and BAC sequences) of the Strongylocentrotus purpuratus genome, Spur_v2.1. None of the contigs have been placed on chromosomes. The Search bar or the BLAST search link above can be used to find annotation or sequence in the assembly. The sequence-based maps for any unplaced contig of interest can then be displayed.

The NCBI Map Viewer provides graphical displays of features on the S. purpuratus genome sequence assembly. Two assemblies are displayed: the reference assembly which is based on the Spur_v2.1 assembly from Baylor, and an alternate assembly, NCBI_super-scaffold_of_Spur_v2.1 produced by NCBI. Map Viewer also provides access to the previous build as well.

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 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 estSpu (i.e. S. purpuratus ESTs and mRNAs) sequence maps. Use the "Maps & Options" window, available on individual chromosome displays, to configure your display.

We know that some mRNA sequences associated with the same GeneID (including RefSeqs) are best placed on multiple contigs. NCBI's annotation process does not permit annotating the same GeneID in more than one location on a build, unless the locus is pseudoautosomal. To alert our users that a particular annotation may not really be a distinct locus, we have elected to display the placement of the mRNA associated with one GeneID associated with the interim (and different) GeneID.

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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