The open source program ID is a natural, synthetic gene sequence.
It is thought that certain bacteria and viruses can cause illness and disease, but the real culprit is the chains of concern that lie within the genomes of these bacteria.
Rice computer scientists and their collaborators developed SeqScreen, a program that screens for short DNA sequences, whether synthetic or natural, to determine their toxicity. Illustrated by Treangen Lab
Calling them out is about to get easier.
Years of work by Rice University computer scientists and their colleagues have resulted in an improved platform for DNA screening and describe the sequence of pathogens, whether naturally occurring or synthetic, before they have a chance to affect public health.
Computer Scientist Todd Treangen by Rice George R. Brown School of Engineering and genomics experts Krista Ternus of Signature Science LLC led the production research SeqScreena program to accurately describe short strands of DNA, commonly known as oligonucleotides.
Todd Treangen. (Provider: Rice University)
Treangen says SeqScreen aims to improve the ability to detect and track a wide range of pathogenic sequences.
“SeqScreen is the first open source software toolkit available for synthetic DNA screening,” says Treangen. “Our program improves upon the previous state of the art for companies, individuals and government agencies in their DNA screening practices.”
Research, starting with high-risk, high-return research funded by the National Intelligence Service IARPA program in 2017, appeared in the magazine Genomic biology.
SeqScreen leveraged the work of partners at Austin, Texas-based Signature Science to manage a database of thousands of gene sequences representing 32 virulence function classes. “This curated database took years of collection and biological review to develop and is at the core of the training data of SeqScreen’s machine learning algorithms,” Treangen said.
The company partnered with Treangen last year to find the SARS-CoV-2 . mutation that may have made omicron variants are more resistant to antibodies, including those from vaccination. “SeqScreen came first and some of its ideas were transferred to the COVID project,” he said. “But SeqScreen has a much broader scope.
“We focused on identifying the functions of the sequences of interest – which we call FunSoC – whereas previous screening methods were more interested in seeing ‘are you this bacterium? are not?’ or ‘are you this virus?’ “SeqScreen doesn’t focus on the name of the bacteria or virus present in your sample. Instead, we want to know if there are sequences in that sample that could be harmful, such as toxins,” said Treangen. can destroy human cells”.
It is important to focus on the functions of interest, he said, because bacteria readily exchange DNA through horizontal gene transfer.
“We’ve highlighted examples of bacteria whose genomes are essentially identical, except that one bacteria has a worrisome sequence, such as a toxin, and the other doesn’t,” says Treangen. . “SeqScreen really relies on the presence or absence of functions representing virulence factors.”
He said SeqScreen will also aid in the detection of new or emerging pathogens from the environment.
Source: Rice University
