Communications of the ACM
Software Speeds Detection of Diseases and Cancer-Treatment Targets
With Sequedex software, a laptop computer can analyze DNA sequences faster than any current DNA sequencer can create them.
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Los Alamos National Laboratory (LANL) researchers say they have developed software that can identify DNA from viruses in all parts of the Tree of Life.
"As part of our testing, we used Sequedex to identify virus sequences in a collaborator's clinical blood sample from Africa," says LANL researcher Ben Mcmahon. "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."
The researchers found the software can identify sequences from viruses and fungi at parts-per-million levels in a sequenced sample. The new version 1.0 edition of Sequedex recognizes patterns in short DNA sequences, and then associates those sequences with phylogeny and the function of the fragment. The researchers say the software classifies fragments 250,000 times faster than conventional methods.
Sequedex uses a list of search terms generated from previously classified genomes to link phylogeny and function to DNA sequences. The researchers note the software has the potential to identify infectious diseases in clinical samples by characterizing the spaces within the human body that are shared by other organisms. Sequedex also can self-update and make plots of its results.
From Los Alamos National Laboratory News
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