First open-source program can enhance detection and monitoring of pathogenic DNA sequences

It is a provided that sure micro organism and viruses may cause sickness and illness, however the actual culprits are the sequences of concern that lie throughout the genomes of those microbes.

Calling them out is about to get simpler.

Years of labor by Rice College pc scientists and their colleagues have led to an improved platform for DNA screening and pathogenic sequence characterization, whether or not naturally occurring or artificial, earlier than they’ve the prospect to impression public well being.

Laptop scientist Todd Treangen of Rice’s George R. Brown College of Engineering and genomic specialist Krista Ternus of Signature Science LLC led the examine that produced SeqScreen, a program to precisely characterize quick DNA sequences, usually known as oligonucleotides.

Treangen mentioned SeqScreen is meant to enhance the detection and monitoring of a variety of pathogenic sequences.

SeqScreen is the primary open-source software program toolkit that’s accessible for artificial DNA screening. Our program improves upon the earlier cutting-edge for corporations, people and authorities companies for his or her DNA screening practices.”

Todd Treangen, Laptop Scientist, Rice’s George R. Brown College of Engineering

The examine, which started as high-risk, high-payoff analysis funded by the Nationwide Intelligence Company’s IARPA program in 2017, seems within the journal Genome Biology.

SeqScreen takes benefit of labor by companions at Austin, Texas-based firm Signature Science to curate a database of hundreds of gene sequences representing 32 varieties of virulence features. “This curated database took years of biocuration and assessment to develop, and is on the core of the coaching knowledge of SeqScreen’s machine studying algorithm,” Treangen mentioned.

The corporate collaborated with Treangen final yr to search out SARS-CoV-2 mutations that will have made the omicron variant extra proof against antibodies, together with these from vaccinations. “SeqScreen got here first, and a few of its concepts carried over to the COVID venture,” he mentioned. “However SeqScreen is far broader in scope.

“We give attention to figuring out features of sequences of concern — which we name FunSoCs — whereas earlier screening approaches have been extra involved with taking a look at ‘are you this bacterium?’ or ‘are you this virus?'” Treangen mentioned. “SeqScreen does not give attention to the names of which micro organism or viruses are in your pattern. Reasonably, we wish to know if there are sequences in that pattern that might be dangerous, corresponding to toxins that may destroy human cells.”

Specializing in features of concern is essential, he mentioned, as a result of micro organism readily change DNA by way of horizontal gene switch.

“We’ve highlighted examples within the publication of micro organism whose genomes are primarily equivalent, besides one has a sequence of concern, corresponding to a toxin, that the opposite doesn’t,” Treangen mentioned. “SeqScreen actually hones in on the presence or absence of features that signify virulence components.”

He mentioned SeqScreen may even support within the detection of novel or rising pathogens from the setting.

Journal reference:

Balaji, A., et al. (2022) SeqScreen: correct and delicate practical screening of pathogenic sequences by way of ensemble studying. Genome Biology. doi.org/10.1186/s13059-022-02695-x.

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