DNA Search Engine for Microbes Launched

Researchers at EMBL's European Bioinformatics Institute have combined their knowledge of bacterial genetics and web search algorithms to build a DNA search engine for microbial data called Bitsliced Genomic Signature Index (BIGSI). The search engine, described in a paper published today in Nature Biotechnology, could enable researchers and public health agencies to use genome sequencing data to monitor the spread of antibiotic resistance genes.

"We were motivated by the problem of managing infectious diseases and antibiotic resistance," explains Zamin Iqbal, research group leader. "We know that bacteria can become resistant to antibiotics either through mutations or with the help of plasmids. We also know that we can use mutations in bacterial DNA as a historical record of bacterial ancestry. This allows us to infer, to some extent, how bacteria might spread across a hospital ward, a country or the world. BIGSI helps us study all of these things at massive scale. For the first time, it allows scientists to ask questions such as 'has this outbreak strain been seen before?' or 'has this drug resistance gene spread to a new species?'."

"This search engine complements other existing tools and offers a solution that can scale to the vast amounts of data we're now generating," explains Phelim Bradley, bioinformatician. "This means that the search will continue to work as the amount of data keeps growing. In fact, this was one of the biggest challenges we had to overcome. We were able to develop a search engine that can be used by anybody with an internet connection."

"As DNA sequencing becomes cheaper, we will see a whole new host of users outside basic research, and a rapid increase in the volume of data generated," continues Iqbal.