Scientists at the Virginia Bioinformatics Institute (VBI) and the Department of Computer Science at Virginia Tech have used high-performance computing to locate small genes that have been missed by scientists in their quest to define the microbial DNA sequences of life. Using an ephemeral supercomputer made up of computers from across the world, the mpiBLAST computational tool used by the researchers took only 12 hours instead of the 90 years it would have required if the work were performed on a standard personal computer.
The new study, reported in the journal BMC Bioinformatics, is the first large-scale attempt to identify undetected genes of microbes in the burgeoning GenBank DNA sequence repository that contains over 100 billion bases of DNA sequence. The genes uncovered may have important functions in the cell, but those functions need to be established by further experiment.
Skip Garner, executive director of VBI and professor of biological sciences at Virginia Tech, commented, "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. These genes may be tomorrow's new targets for pharmaceutical research, for example to find new antibiotics or vaccines, which is extremely important since we need novel approaches to combat the emergence of new drug-resistant bugs."
In the past few years, enormous progress has been made in sequencing technologies that allow scientists to produce astonishing amounts of sequence data. Today more than 1200 genome sequences of microbes are housed in the GenBank database. By far one of the biggest problems facing scientists is not generating the sequence data but reliably locating and assigning a function to the many genes in a genome, a process that scientists refer to as annotation. This process crucially depends on sophisticated computational tools. The field of bioinformatics is c
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