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Rock Snot Genomics


A colony of Berkeleya rutilans diatoms.

A colony of Berkeleya rutilans diatoms, marine diatoms that live and divide in mucilaginous tubes they secrete.

Credit: Matt Ashworth, The University of Texas at Austin

University of Texas at Austin researchers are using the Ranger supercomputer to align, organize, and analyze diatom DNA data. The researchers want to understand what the diatom's original ancestor might have looked like.

"There's this idea that the early diatom was a small flagellate, but what we're finding at the base of the diatom tree are things that are long and tubular, much like the tube inside of a paper towel roll," says University of Texas at Austin professor Edward Theriot.

Ranger saves the researchers time in analyzing the data and enables them to test alternative hypotheses. "With Ranger, we can redirect our time away from just finding the best tree for a dataset, towards asking how different that best tree is from what scholars thought about diatom evolution, say, 100 years ago," Theriot says.

University of Texas at Austin professor Edward Theriot says Ranger is a powerful tool for analyzing DNA. "There are a number of programs that compare DNA sequences and estimate how those DNA sequences evolved from each other, and some of these have very complex algorithms," Ashworth says. "Before we had access to Ranger it would take weeks and months to run. Ranger does the same analyses in hours."

From Texas Advanced Computing Center
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Abstracts Copyright © 2013 Information Inc., Bethesda, Maryland, USA


 

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