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Genomic variation easier to identify with UCSD/Brown software

e created is a more accurate tool for detecting microinversions," said Benjamin Raphael, an assistant professor of computer science at Brown and a member of the University's Center for Computational Molecular Biology. "This software will be very useful for comparative genomics studies and help biologists better understand how genomes evolved over time."

Work on InvChecker was spearheaded at UCSD. Mark Chaisson, a graduate student in UCSD's Jacobs School of Engineering, was lead author of the journal article. Pavel Pevzner, a UCSD computer science and engineering professor, served as senior scientist on the project.

Chaisson, Pevzner and Raphael put the software to an ambitious test. They chose a small region of the mammalian genome, called the CFTR region, for study. The scientists chose the CFTR region because it is well studied and widely shared among mammals. They searched for microinversions in this region in the genomes of 15 mammals from human and chimp to cow and dog to possum and hedgehog and found that these mutations were found in all species and occur frequently.

The team then used the results to reconstruct an evolutionary tree showing the relationship between these species a tree strikingly similar to ones created with much more extensive molecular or morphological information.

"What was amazing is that we could accurately trace the evolution of these species simply by studying tiny mutations in a very small region of the genome," Raphael said. "This really shows that the method works."

The team also used InvChecker to study the genetic differences between humans and chimpanzees. They discovered 167 new microinversions in humans and chimps, and they found that 80 percent of microinversions previously proposed for these species were actually different types of mutations.


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Contact: Wendy Lawton
Wendy_Lawton@brown.edu
401-863-1862
Brown University
22-Dec-2006


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