Texas A&M researchers develop tool to study complex cluster...( COLLEGE STATION July 2 2008 -- Two T...)

COLLEGE STATION, July 2, 2008 -- Two Texas A&M University researchers have developed a computational tool that will help scientists more accurately study complex units of clustered genes, called operons, in bacteria. The tool, which allows scientists to analyze many bacterial genomes at once, is more accurate than previous methods because it starts from experimentally validated data instead of from statistical predictions, they say. The researchers hope their tool will lead to a better understanding of the complex genetic mechanisms involved in a cell's functioning.

"It's a very complicated mechanism inside a cell that makes the whole thing work, and operons are one of the important components in this process," said Sing-Hoi Sze, Texas A&M computer science, biochemistry and biophysics researcher. "We want to understand how these genetic mechanisms work because DNA codes proteins, and proteins are what make up everything in your body. In order to understand the genetic processes in more complex organisms, we have to start with the simpler organisms like bacteria."

Sze and his colleague, computer science researcher Qingwu Yang, detail their computational tool and its implications in their paper published in the journal Genome Research.

An operon is a unit of genes that are clustered together and have similar functions, Sze said. Genes are controlled by a mechanism called a promoter, which turns the genes on or off. In higher organisms, like humans, there is usually a specific promoter that controls each gene separately, Sze explained. However, a bacteria's genome has to be compact, so there are a lot of genes clustered close together that are controlled by the same promoter, and this set of genes is called an operon.

Different species of bacteria have similar genes, but their genes may not have the same layout or clustering pattern, so their operons may function differently, Sze said. Scientists want to understand how the operons in each specie
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