Two-Hit Filter Synthesis for Genomic Database Search

Abstract

Advancements in genomic sequencing technology is causing genomic database growth to outpace Moore's Law. This continues to make genomic database search a difficult problem and a popular target for emerging processing technologies. The de facto software tool for genomic database search is NCBI BLAST, which operates by transforming each database query into a filter that is subsequently applied to the database. This requires a database scan for every query, fundamentally limiting its performance by I/O bandwidth. In this paper we present a functionally-equivalent variation on the NCBI BLAST algorithm that maps more suitably to an FPGA implementation. This variation of the algorithm attempts to reduce the I/O requirement by leveraging FPGA-specific capabilities, such as high pattern matching throughput and explicit on chip memory structure and allocation. Our algorithm transforms the database -- not the query -- into a filter that is stored as a hierarchical arrangement of three tables, the first two of which are stored on chip and the third off chip. Our results show that -- while performance is data dependent -- it is possible to achieve speedups of up to 8X based on the relative reduction in I/O of our approach versus that of NCBI BLAST. More importantly, the performance relative to NCBI BLAST improves with larger databases and query workload sizes.