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Speed Search

Researchers from the University of Oxford have devised a way to quickly search through viral and bacterial genomes, the Atlantic reports.

This effort, it notes, was spurred by the discovery of colistin resistance among pigs in China in 2015, and public health officials in the UK wanted to know if colistin resistance genes were present there, too. But it took 256 computers a weekend to comb through the data, the European Bioinformatics Institute's Zamin Iqbal tells the Atlantic. He and his colleagues sought to speed that process up.

As they report in Nature Biotechnology this week, the researchers developed BItsliced Genomic Signature Index (BIGSI), which pools together microbial population genomics data and web-searching tools. With this, they indexed 447,833 bacterial and viral whole-genome sequence datasets and searched through it for colistin resistance genes, a search that took less than two seconds.

The researchers caution in their paper that this is a k-mer index with related limitations, and at the Atlantic, Kent State University's Tara Smith notes that the searches will only be as good as the data indexed. The researchers further add in their paper that they will be updating it with new sequences.