Machine learning approach significantly expands inovirus diversity

phys.org | 7/22/2019 | Staff
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To answer the question, "Where's Waldo?" readers need to look for a number of distinguishing features. Several characters may be spotted with a striped scarf, striped hat, round-rimmed glasses, or a cane, but only Waldo will have all of these features.

As described July 22, 2019, in Nature Microbiology, a team led by scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, developed an algorithm that a computer could use to conduct a similar type of search in microbial and metagenomic databases. In this case, the machine "learned" to identify a certain type of bacterial viruses or phages called inoviruses, which are filamentous viruses with small, single-stranded DNA genomes and a unique chronic infection cycle.

Way - Viruses - Study - Author - Simon

"We're not sure why we systematically manage to miss them; maybe it's due to the way we currently isolate and extract viruses," said the study's lead author Simon Roux, a JGI research scientist in the Environmental Genomics group.

Inoviruses are stealth agents that can enter and exit through the cell membrane without lysing the bacterial host. They can also influence their host's growth and pathogenicity, in turn affecting the microbe's own eukaryote host. As their small genomes can be easily manipulated through genetic engineering, inoviruses are used for several biotechnological applications, most notably, phage display. The search tool Roux and his colleagues developed first worked on a reference dataset that included genome sequences known to be affiliated with the Inoviridae. "What we're really doing is looking for a particular gene found in all inoviruses, and then checking the surrounding genes," he said. "If these genes are similar in size and function to those in typical bacterial or archaeal genomes, the sequence is most likely not an inovirus. But if these nearby genes are both short and novel, then...
(Excerpt) Read more at: phys.org
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