BLASTP-ACC: Parallel Architecture and Hardware Accelerator Design for BLAST-Based Protein Sequence Alignment

• Published in: IEEE transactions on biomedical circuits and systems Vol. 13; no. 6; pp. 1771 - 1782
• Main Authors: Li, Yu-Cheng, Lu, Yi-Chang
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.12.2019; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithms; Alignment; Amino Acid Sequence; Amino acids; Basic Local Alignment Search Tool (BLAST); Biotechnology; Computer architecture; Databases, Factual; Equipment Design; Field programmable gate arrays; FPGA; Hardware; hardware accelerator; Heuristic algorithms; Nucleotide sequence; parallel architecture; Protein sequence; protein sequence alignment; Proteins; Proteins - genetics; Queries; Query processing; Sequence Alignment - instrumentation; Sequence Alignment - methods; Sequences; Smith–Waterman
• ISSN: 1932-4545; 1940-9990; 1940-9990
• DOI: 10.1109/TBCAS.2019.2943539

In this study, we design a hardware accelerator for a widely used sequence alignment algorithm, the basic local alignment search tool for proteins (BLASTP). The architecture of the proposed accelerator consists of five stages: a new systolic-array-based one-hit finding stage, a novel RAM-REG-based two-hit finding stage, a refined ungapped extension stage, a faster gapped extension stage, and a highly efficient parallel sorter. The system is implemented on an Altera Stratix V FPGA with a processing speed of more than 500 giga cell updates per second (GCUPS). It can receive a query sequence, compare it with the sequences in the database, and generate a list sorted in descending order of the similarity scores between the query sequence and the subject sequences. Moreover, it is capable of processing both query and subject protein sequences comprising as many as 8192 amino acid residues in a single pass. Using data from the National Center for Biotechnology Information (NCBI) database, we show that a speed-up of more than 3× can be achieved with our hardware compared to the runtime required by BLASTP software on an 8-thread Intel Xeon CPU with 144 GB DRAM.