TY - GEN
T1 - FPGA-accelerated seed generation in Mercury BLASTP
AU - Jacob, Arpith
AU - Lancaster, Joseph
AU - Buhler, Jeremy
AU - Chamberlain, Roger D.
PY - 2007
Y1 - 2007
N2 - BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we focus on seed generation, the first stage of the BLASTP algorithm. Our seed generator is capable of processing database residues at up to 219 Mresidues/second for 2048-residue queries. The full Mercury BLASTP pipeline, including our seed generator, achieves a speedup of 37x over the popular NCBI BLASTP software on a 2.8 GHz Intel P4 CPU, with sensitivity more than 99% that of the software. Our architecture can be generalized to accelerate the seed generation stage in other important biocomputing applications.
AB - BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we focus on seed generation, the first stage of the BLASTP algorithm. Our seed generator is capable of processing database residues at up to 219 Mresidues/second for 2048-residue queries. The full Mercury BLASTP pipeline, including our seed generator, achieves a speedup of 37x over the popular NCBI BLASTP software on a 2.8 GHz Intel P4 CPU, with sensitivity more than 99% that of the software. Our architecture can be generalized to accelerate the seed generation stage in other important biocomputing applications.
UR - https://www.scopus.com/pages/publications/47349112881
U2 - 10.1109/FCCM.2007.11
DO - 10.1109/FCCM.2007.11
M3 - Conference contribution
AN - SCOPUS:47349112881
SN - 0769529402
SN - 9780769529400
T3 - Proceedings 2007 IEEE Symposium on Field-Programme Custom Computing Machines, FCCM 2007
SP - 95
EP - 104
BT - Proceedings 2007 IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2017
PB - IEEE Computer Society
T2 - 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2007
Y2 - 23 April 2007 through 25 April 2007
ER -