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How to Catch a Fish Genome With Big Data


A California Yellowtail.

Researchers have assembled an annotated genome of the California Yellowtail for the first time.

Credit: friendsoflajollashores.com

Researchers from the U.S. National Marine Fisheries Service, Iowa State University, and Mexico's National Polytechnic Institute have for the first time assembled an annotated genome of the California Yellowtail, using the eXtreme Science and Engineering Discovery Environment (XSEDE).

The genomic assembly was initially computed at the Pittsburgh Supercomputing Center on the Blacklight system, says Iowa State University's Andrew Severin. He also notes XSEDE's Stampede supercomputer at the Texas Advanced Computing Center was used "to do the annotation of these gene models that we identified in the genome to try and figure out what their functions are. That required us to perform an analysis called the Basic Local Alignment Search Tool [BLAST], and it required us to use many [central-processing units], over a year's worth of compute time that we ended up doing within a couple of week's worth of actual time because of the many nodes that were on Stampede."

From Texas Advanced Computing Center
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