Software can now identify DNA from viruses and speed up diagnoses

Sequedex software from Los Alamos National Laboratory can slash the time it takes to diagnose some illnesses from weeks to hours

dna methylation
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Los Alamos National Laboratory (LANL) announced this week that bioinformatics software it created can now identify DNA from fungi, bacteria, viruses and other pathogens, slashing the time it takes to diagnose some illnesses from weeks to hours.

The software can also speed the analysis of cancerous tumor genetics for chemotherapy options and prognosis.

The LANL's new version of its Sequedex software recognizes patterns in short DNA sequences and then associates those sequences with phylogeny -- the genetic evolution of an organism. It examines a collection of DNA fragment sequences "in a similar fashion to doing a search in a web browser," Los Alamos said in a statement.

For example, in Google, entering the search terms "plumber," "Smith," and "Chicago" might return links to plumbers named Smith in the Windy City; similarly, Sequedex uses a list of search terms generated from previously classified genomes to link phylogeny and function to DNA sequences.

tree labels Wikipedia Commons

This image is of an evolutionary tree— a so-called "Tree of Life"— showing the divergence of modern species from their common ancestor in the center. The three domains are colored, with bacteria blue, archaea green and eukaryotes red.

"The search terms generated by Sequedex are selected by evolution in the sense that they must be present in more than one genome. Each term is also linked to a branch of the Tree of Life and a set of one or more biological functions," the Lab said.

Sequedex classifies those DNA fragments 250,000 times faster than conventional methods. With Sequedex, a laptop computer can analyze DNA sequences faster than any current DNA sequencer can create them.

The software, the Lab said, can place a pathogen into its proper place in the evolutionary "Tree of Life," That, in turn, can help finger pathogen-caused diseases, aid with a selection of therapeutic targets for cancer treatment, and improve yields of algae farms within relatively easy reach for health-care professionals, researchers and others.

"As part of our testing, we used Sequedex to identify virus sequences in a collaborator's clinical blood sample from Africa," Ben McMahon, a scientist in Los Alamos's Theoretical Biology and Biophysics group, said. "In the course of an afternoon, the software had identified a deadly rabies virus, something that would have taken weeks of work using conventional methods. Sequedex software can now identify sequences from viruses and fungi at parts-per-million levels in a sequenced sample."

Copyright © 2014 IDG Communications, Inc.

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