DNA databases: New method cuts indexing from weeks to hours, searches to minutes

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2021-06-29 20:00:11

June 28, 2021

by Rice University

Rice University computer scientists are sending RAMBO to rescue genomic researchers who sometimes wait days or weeks for search results from enormous DNA databases.

DNA sequencing is so popular, genomic datasets are doubling in size every two years, and the tools to search the data haven't kept pace. Researchers who compare DNA across genomes or study the evolution of organisms like the virus that causes COVID-19 often wait weeks for software to index large, "metagenomic" databases, which get bigger every month and are now measured in petabytes.

RAMBO, which is short for "repeated and merged bloom filter," is a new method that can cut indexing times for such databases from weeks to hours and search times from hours to seconds. Rice University computer scientists presented RAMBO last week at the Association for Computing Machinery data science conference SIGMOD 2021.