Hyper customized processors for bio-sequence database scanning on FPGAs
Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
A programmable array processor architecture for flexible approximate string matching algorithms
Journal of Parallel and Distributed Computing
Families of FPGA-based accelerators for approximate string matching
Microprocessors & Microsystems
| Hi-index | 0.00 |
In the paper, we present storage optimization scheme for hardware accelerating Needleman-Wunsch algorithm. The scheme exploits the characteristics of back-tracking phase in which the back-trace path only travels in a constrained area. Our analysis shows that in addition to logic element resource and memory capacity, the number of RAM blocks is also one of the constrained factors for hardware accelerating bio-sequence alignment. The optimized algorithm only store part of the score matrix to reduce storage usages of FPGA RAM blocks, and implement more processing element in FPGA. We fit our design on FPGA chips EP2S130 and XC2VP70. The experimental results show that the peak performance can reach 77.7 GCUPS (Giga cell updates per second) and 46.82 GCUPS respectively. Our implementation is superior to related works in clock frequency, the maximal PE number and peak performance, respectively.