Open source software that identifies naturally occurring synthetic genetic sequences

SeqScreen can reveal DNA

Pc scientists at Rice College and their collaborators have developed SeqScreen, a program that screens quick DNA sequences, whether or not artificial or pure, to find out their toxicity. Credit score: Treangen Lab/Rice College

Admittedly, some micro organism and viruses may cause sickness and illness, however the actual perpetrator is the sequence of concern that lies inside the genomes of those microbes.

Summoning them is about to get simpler.

Years of labor by Rice College pc scientists and colleagues has improved the DNA screening platform and characterization of pathogenic sequences, whether or not man-made or natural, earlier than that they had an opportunity to have an effect on public well being.

Pc scientist Todd Trengen of the George R. Brown Faculty of Engineering at Rice and genomics specialist Krista Ternus of Signature Science LLC led the examine that produced SeqScreen, a program to precisely characterize quick DNA sequences, usually referred to as oligonucleotides.

Trengen stated the aim of SeqScreen is to enhance detection and monitoring of a variety of disease-causing sequences.

“SeqScreen is the primary open supply software program toolkit obtainable for artificial DNA screening,” Trengen stated. “Our program improves the prior state of corporations, people and authorities companies for his or her DNA screening practices. “

The examine, which started as a high-risk, high-reward analysis mission, was featured within the journal genome biology.

SeqScreen leverages the work of companions at Austin, Texas-based Signature Science to prepare a Database 1000’s of genetic sequences representing 32 kinds of virulence features. “This curated database has taken years of dynamic configuration and revision to develop, and is on the core of the coaching information for SeqScreen’s machine studying algorithm,” Trengen stated.

The corporate teamed up with Treangen final 12 months to seek out the SARS-CoV-2 mutations which will have made the Omicron variant extra immune to antibodies, together with these present in vaccines. “SeqScreen got here first, and a few of its concepts have moved to the COVID mission,” he stated. “However SeqScreen is a wider scope.”

“We’re centered on figuring out the features of sequences of concern – which we name FunSoCs – whereas earlier screening approaches have been extra concerned with ‘Are you these micro organism?’ Or are you that virus?” “SeqScreen doesn’t deal with the names of micro organism or viruses in your pattern. As a substitute, we wish to see if there are sequences in that pattern that could possibly be dangerous, similar to toxins that may destroy human cells.”

Specializing in the features of concern is vital, he stated, as a result of micro organism simply alternate DNA by them horizontal gene switch.

“We’ve got highlighted examples in propagating micro organism whose genomes are basically equivalent, besides that one has a cascade of concern, similar to a toxin that the opposite doesn’t,” Trengen stated. “SeqScreen actually focuses on the presence or absence of features which might be virulence components.”

He stated SeqScreen can even assist detect new or rising pathogens from the surroundings.

Pc scientists develop software program to seek out ‘low frequency’ variants in sequencing information

extra data:
Advait Balaji et al, SeqScreen: correct and delicate useful screening of disease-causing sequences by group studying, genome biology (2022). DOI: 10.1186 / s13059-022-02695-x

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