LISA: Towards Learned DNA Sequence Search

Understand

Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics.

• Genomics data analytics at this scale requires overcoming performance bottlenecks, such as searching for short DNA sequences over long reference sequences.
• In this paper, we introduce LISA (Learned Indexes for Sequence Analysis), a novel learning-based approach to DNA sequence search.
• As a first proof of concept, we focus on accelerating one of the most essential flavors of the problem, called exact search.