Open source program identifies natural and synthetic genetic sequences

SeqScreen may reveal 'worrying' DNA

Laptop scientists at Rice College and their collaborators have developed SeqScreen, a program for screening brief DNA sequences, whether or not artificial or pure, for toxicity. Credit score: Treangen Lab/Rice College

It’s a indisputable fact that sure micro organism and viruses could cause sickness and illness, however the true culprits are the worrisome sequences discovered throughout the genomes of those microbes.

Calling them is about to get simpler.

Years of labor by pc scientists at Rice College and their colleagues have led to an improved platform for DNA detection and characterization of pathogenic sequences, whether or not man-made or natural, earlier than they’ve an opportunity to have an effect on public well being. .

Laptop scientist Todd Treangen of Rice’s George R. Brown College of Engineering and genomics specialist Krista Ternus of Signature Science LLC led the research that produced SeqScreen, a program for exactly characterizing brief sequences of DNA, usually referred to as oligonucleotides.

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

“SeqScreen is the primary open supply software program toolkit that’s accessible for artificial DNA detection,” stated Treangen. “Our program improves the earlier cutting-edge for firms, people and governmental businesses for his or her DNA detection practices.

The research, which started as a high-risk, high-yield analysis venture, seems within the journal genome biology.

SeqScreen leverages the work of companions at Austin, Texas-based firm Signature Science to create a database of hundreds of gene sequences representing 32 varieties of virulence features. “This curated database took years of bio-curating and overview to develop, and is the core of the coaching information for SeqScreen’s machine studying algorithm,” Treangen stated.

The corporate collaborated with Treangen final yr to seek out SARS-CoV-2 mutations which will have made the Omicron variant extra proof against antibodies, together with these in vaccines. “SeqScreen got here first and a few of his concepts carried over into the COVID venture,” he stated. “However SeqScreen has a much wider scope.”

“We targeted on figuring out the features of the sequences of curiosity, which we name FunSoCs, whereas earlier screening approaches had been extra involved with ‘are you this micro organism?’ or ‘are you this virus?'” Treangen stated. “SeqScreen does not deal with the names of what micro organism or viruses are in your pattern. Relatively, we need to know if there are sequences in that pattern that could possibly be dangerous, similar to toxins that may kill human cells.”

It is essential to deal with the features of curiosity, he stated, as a result of micro organism readily trade DNA throughout horizontal gene switch.

“We’ve got highlighted examples within the publication of micro organism whose genomes are basically an identical, besides one has a sequence of concern, similar to a toxin, that the opposite doesn’t,” Treangen stated. “SeqScreen actually zeroes in on the presence or absence of options that signify virulence elements.”

He stated that SeqScreen may also assist in the detection of latest or rising pathogens from the surroundings.

Laptop scientists develop a program to seek out ‘low-frequency’ variants in sequence information

Extra data:
Advait Balaji et al, SeqScreen: Correct and delicate useful detection of pathogenic sequences by means of ensemble studying, genome biology (2022). DOI: 10.1186/s13059-022-02695-x

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Quotation: Open supply program identifies pure and artificial genetic sequences (June 21, 2022) Retrieved June 21, 2022 at -gene.html

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