International Mammalian Genome Society

The 15th International Mouse Genome Conference (2001)


Dr Deanna Church
Building 38A, rm6S614K
8600 Rockville Pike
Bethesda 20984 USA

Co-Authors: Maglott D, Shkeda A, Chen H-C, Schuler GD
Institution: National Institute of Biotechnology Information

Currently, there are greater than 17 million Whole Genome Shotgun (WGS) reads from C57BL6/J, representing roughly 3-fold coverage of the mouse genome. In addition, more than 400 Mb of sequence from greater than 2300 accessioned clones is also available. The majority of this sequence is contained within HTGS phase 1 sequence (322 Mb in 1696 accessions). The average phase 1 accession contains 24 fragments, with an average fragment length of 7.7 Kb. HTGS phase 3 sequences are being assembled into non-redundant, annotated sequence contigs. Our effort to assemble and annotate mouse genomic sequence will be discussed. The WGS reads are currently being assessed for quality, repeat-content, pairing rates. In addition, these WGS are being compared to the human genome. When using well-annotated regions of the genome, there are currently as many sequence alignments in non-coding regions as there are in coding regions.

In addition to analyzing genomic sequence, we have been utilizing mRNA sequences found in LocusLink, EST sequences found in UniGene, and curated information from the Mouse Genome Database (MGD) to establish orthologs relationships between human and mouse. Using the human draft sequence as a guide, we have built human-mouse homology maps using two different human genome assemblies and two different mouse maps. The utility of the conserved synteny map as a tool to assess genome assemblies, as well as the virtual mapping of >3000 mouse genes will be discussed.

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