In December 2004, the Drosophila Genome Project at the Baylor College of Medicine released Dpse_2.0, an update to the version 01 assembly of the genome sequence of Drosophila pseudoobscura, which was subsequently published in the journal Genome Research. The genome was sequenced to 9.1x coverage and assembled into 16 ultra-scaffolds anchored on the six chromosome arms. Chromosomes 2 and 3 are represented by single ultra-scaffolds, whereas the chromosome XL, XR, and 4 assemblies are currently composed of 4, 4, and 5 scaffolds, respectively.

The NCBI Map Viewer provides graphical displays of features on the D. pseudoobscura genome sequence assembly, including the September 2008 release 2.3 gene annotation provided by FlyBase. 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, ESTs, and DNA clones. The ab initio map includes Gnomon predicted gene models calculated in July 2009. Further documentation is provided through the links below to describe the resource features and methods used, tutorials, and statistics.

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 contig of interest can then be displayed. Results are indicated both graphically, as tick marks on the chromosome diagrams, 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 gene models), and rnaDm (i.e. Drosophila melanogaster ESTs and mRNAs) sequence maps. Use the "Maps & Options" window to configure each display.

Other genomes can also be viewed in the NCBI Map Viewer. The Map Viewer home page provides a current list. 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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