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Rough rodent: the public consortium has announced an early draft of the mouse genome. Credit: TEK IMAGE/SPL

Public genome sequencers say they have met the goal they set for themselves last October, by producing crude sequencing data for almost the entire mouse genome.

But they haven't yet figured out how to finish the project to the level of accuracy they would like to see, which would mean sequencing each base in the genome an average of 10 times over.

The Mouse Sequencing Consortium has been using the high-throughput 'shotgun' method pioneered by the private company Celera Genomics of Rockville, Maryland. This technique involves sequencing some 6 million fragments, each between 500 and 700 bases long, of the mouse genome and then assembling them later.

The public consortium says it has now sequenced 94% of the genome, hitting each base an average of three times. But the sequence data remain almost completely unassembled. The public database contains more than 15 million unordered fragments.

The consortium's announcement came just 10 days after Celera revealed that it had completed and assembled 2.6 billion bases of the mouse genome (Nature 411, 8; 2001). Unlike the Celera data, the public data are available free to all researchers.

But the next phase of the project remains undefined. This was the plan all along, says Jane Peterson, a project official at the National Human Genome Research Institute (NHGRI), because the partial sequence data will be useful in working out which techniques to use to complete the genome.

Three corporate sponsors paid a quarter of the $58 million cost of the initial phase. But so far no arrangements have been made for continued private support of the project. And although the NHGRI has ample funds to continue sequencing the mouse, no budgets for the next phase have yet been set.

“At this point we are shifting strategies,” says Robert Waterston, director of the Washington University genome sequencing centre. “We are developing plans to get the complete genome sequence.”