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UPDATE: Consortium Says Mouse Genome Two-Thirds Complete

This story has been updated from a previous version.

NEW YORK, Feb 15 – Just three days after Celera announced it had assembled and sequenced the mouse genome, the publicly and privately funded Mouse Sequencing Consortium said Thursday it had achieved 66 percent coverage of the genome and plans to have 93 to 95 percent coverage by the beginning of April.  

The consortium will then work to assemble the draft sequence during the month of April, said Arthur Holden, Chairman of the Mouse Sequencing Consortium. “The plan is that we do 3X coverage using a whole genome shotgun approach, sequence plasmids from both ends, then align those ends, in the same way that the human sequence was assembled by Celera and the Human Genome Project.” 

To read the assembly, the Consortium plans to develop a mouse equivalent of Golden Path, the human genome browser developed by James Kent at the University of California Santa Cruz.

This mouse sequence, which includes over 6.5 million deposited traces, is publicly available in an NCBI data repository and on the Sanger Center’s Ensembl system, but remains in unassembled fragments, said Mary Prescott, a spokeswoman for the Mouse Sequencing Consortium.  

The consortium, which consists of scientists from Affymetrix, GlaxoSmithKline, the Merck Genome Research Institute, the US National Institutes of Health, and the Wellcome Trust, was formed in October 2000 to produce a publicly available mouse sequence in six months. 

The consortium is sequencing the “black six” or C57BL6/J mouse. Celera, which began sequencing the mouse last April, said Monday it had sequenced 15.8 million base pairs for 5.5X, or 99 percent, coverage of the genome for three strains of mouse: the 129/SvJ, DBA/2J, and A/J.     

The raw reads are being deposited every week in the NCBI and Ensembl data repositories, which also contain the more finished sequence.  The raw data has been checked for quality with positive results, the consortium said, and can be accessed at http://www.ncbi.nlm.nih.gov/Traces/trace.cgi   and http://trace.ensembl.org

Additionally, researchers can use megaBlast and SSHA to compare sequences and mouse traces, and to download mouse traces, the consortium said 

 

 

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