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UC Berkeley Team Gives Whole Genome Shotgun a Leg Up

COLD SPRING HARBOR, NY, May 9 - A team from the University of California at Berkeley says it has slapped a second barrel onto the whole genome shotgun.

 

Speaking at Cold Spring Harbor Lab's 2002 Genome Sequencing & Biology meeting here this morning, Lior Pachter outlined his groups' method of improving results generated from whole genome shotgun assemblers like ARACHNE.

 

The process, which Pachter claims can significantly reduce the number of supercontigs in ARACHNE assemblies, has three steps: First, one takes the contigs of an assembly and uses BLAT/AVID to align them to the reference genome. The next step is to create faux paired reads that implicitly contain data about the order and orientation of the contigs.

 

Finally, one includes the faux pairs into another round whose results, Pachter says, will be improved. Pachter, who said the cycle can be iterated, added that his team has ordered and oriented all draft primate sequence data in Genbank.

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