Boosting Backward Search Throughput for FM-Index Using a Compressed Encoding

Abstract

The rapid development of DNA sequencing technologies has demanded for compressed data structures supporting fast pattern matching queries. FM-index is a widely-used compressed data structure that also supports fast pattern matching queries. It is common for the exact matching algorithm to be memory bound, resulting in poor performance. We propose a new data-layout of FM-index that compacts all data needed to perform the searching process. This results in an improvement of the search computing time for genomic data.