Blog: High-Performance Computing Reveals Missing Genes

High-Performance Computing Reveals Missing Genes
Virginia Bioinformatics Institute (04/13/10) Whyte, Barry

Researchers at Virginia Tech's (VT's) Department of Computer Science and the Virginia Bioinformatics Institute used a supercomputer to locate small genes that have been overlooked by scientists in their search for the microbial DNA sequences of life. The researchers used the mpiBLAST computational tool, which enabled them to conduct the study in 12 hours, instead of the 90 years it would have taken using a standard personal computer. The researchers say the study is the first large-scale attempt to identify undetected genes of microbes in the GenBank DNA sequence repository, which currently contains more than 100 billion bases of DNA sequences. "This is a perfect storm, where an overwhelming amount of data is analyzed by state-of-the-art computational approaches, yielding important new information about genes," says VT professor Skip Garner. There are currently more than 1,200 genome sequences of microbes stored in the GenBank database. "To facilitate the rapid discovery of missing genes in genomes, we used our mpiBLAST sequence-search tool to perform an all-to-all sequence search of the 780 microbial genomes that we investigated," says VT professor Wu Feng.

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