In May 2006 the Genome Sequencing Center at the Washington University School of Medicine in St. Louis submitted an improved 6.6X draft chicken genome assembly. The chicken genome, the first avian genome to be sequenced, has a haploid genome size of 1200 Mb. The chicken genome, similar to other avian genomes, is composed of chromosomes of vastly different sizes identified as either macro- or microchromosomes. The Gallus gallus genome has 38 pairs of autosomes and a pair of sex chromosomes, referred to as Z and W to distinguish them from mammalian sex chromosomes. In birds, the male is homozygous (ZZ) while the female is heterozygous (ZW).

In the first assembly, chromosome 25 (identified as LGE26C13) was not represented but it is represented in this improved assembly. Two linkage groups (LG) remain: LGE64 and LGE22C19W28_E50C23, which represents a merge of LGE22C19W28 and LGE50C23. Extensive documentation is provided to describe the resource features and methods used, tutorials, and statistics.

Data for other avian species has also been mapped to the current chicken assembly. Separate maps for zebra finch Taeniopygia guttata UniGene clusters and mRNAs, as well as mRNAs from avian species other than chicken and zebra finch are available.

The NCBI Map Viewer provides graphical displays of features on the chicken genomic sequence assembly as well as genetic and physical maps. The first assembly introduced a significant modification to NCBI's gene modeling by including the annotation of partial as well as predicted genes. Annotation of partial genes is also included in this improved assembly.

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.

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 (e.g., the Gnomon predicted models), and UniGene 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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