The NCBI Map Viewer displays a graphical view of Zv7, the seventh release of the zebrafish genome sequence provided by the Wellcome Trust Sanger Institute in July 2007. This release is tied to the April 11, 2007 FPC map and contains more than 1 GB of sequence from 7,823 BAC clones. Lower quality whole genome shotgun (WGS) sequence from a single Tuebingen, doubled haploid zebrafish is used to fill gaps in the tiling path provided by the FPC map. In this assembly, more than 200MB of erroneously duplicated sequence has been removed, compared to Zv6, although the Sanger Institute notes that this release remains a preliminary assembly. The NCBI zebrafish build 3.1 includes the Zv7 assembly, an annotation update, and the complete mitochondrial genome of a strain ABC zebrafish.

Zebrafish has 25 pairs of chromosomes. According to an agreement reached at the European Zebrafish Meeting in Paris, 2003, linkage group numbers are translated directly into chromosome numbers (e.g. linkage group 1 is equal to chromosome 1).

The NCBI Map Viewer provides graphical displays of features on the Zv7 assembly. Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map), the BAC and WGS sequences (the 'Component' map), and the location of genes, STSs, ESTs, and Gnomon predicted gene models. In collaboration with ZFIN and members of the zebrafish community, Map Viewer also displays genetic maps (GAT, HS, MGH, MOP, and ZMAP) and radiation hybrid maps (LN54 and T51). Extensive documentation is provided to describe the resource features and methods used, as well as tutorials and statistics.

You can find genes or markers of interest by submitting a query against the whole genome or against one 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 is viewable in the context of additional data. For genes, a particularly useful display includes the Gene, Ab initio (i.e. the Gnomon predicted models), and rnaDr (i.e. zebrafish 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.

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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