International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


Church DM, Annotation Team NCBI

NIH/NCBI, Bethesda, United States

Genomic resources for the mouse genome have increased greatly. A Whole Genome Shotgun (WGS) assembly generated by the Mouse Genome Sequencing Consortium (MGSC) was released and published. During the past year, sequencing resources for mouse have shifted towards clone-based (HTGS) sequence. As of June 4, 2004, 1.48 Gb of non-redundant finished sequence and 1.8 Gb of redundant draft sequence were available. Greater than 95% of the HTGS sequence is from the reference strain (C57BL/6J). To leverage all available sequence data, NCBI has been performing composite assemblies that integrate HTGS sequence from C57BL/6J into the MGSCv3. NCBI Build 33 (based on data from May 30, 2004) integrated 1.1 Gb of HTGS phase 3 (finished) sequence.. In addition to producing the reference assembly, NCBI has been producing alternate, strain-specific assemblies. In Mouse Build 33, 6 alternate assemblies were produced. In addition, the publicly available portion of the Celera mouse assembly (Mmu16) is annotated and available as part of the standard NCBI resource set:, Map Viewer, the NCBI ftp site, Entrez Gene, etc.

In addition to producing these assemblies, NCBI provides annotation for all assemblies via a suite of software tools available from our website ( Current annotation provides prediction of gene models (based on alignment and ab initio prediction), clone placement (BACs and fosmids based on end sequence alignment), variation, STSs, Gene Trap clones, human and rat transcripts and phenotypes (via STS connections). Annotation information will be provided for the current mouse assemblies. In addition, improvements in the NCBI MapViewer and associated resources with respect to clone identification and comparative mapping will be discussed.

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