RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation

Abstract

Basic Local Alignment Search Tool (BLAST) is

FPGA based architecture for DNA sequence comparison and database search

“…al. [15] is the only group that did actual runs of BLAST algorithm in FPGAs to date but their results proved worse than software implementations due to I/O problems, PCI bottleneck and the old technology (XC 4085) which they used (the performance was five times slower than the purely software version). For that reason their results are not used in this comparison.…”

“…Mapping dynamic programming algorithms on FPGAs seems to be suitable for the capabilities of FPGAs especially when systolic array architectures are used. On the other hand, mapping the BLAST algorithm on reconfigurable logic is not as suitable and only in [15] an implementation can be found. In this architecture Muriki et al measured the time allocation for BLAST execution in software and according to their measurements replaced the code segment that consumes almost 80% of execution time with a system call to their specific hardware.…”

“…These calculations produce substantial computing load but the most significant part of the computation power is consumed to find every HSP and extend it, calculating its score. Previous efforts for hardware implementation of BLAST using profiling show that almost 80% of CPU time is spent on these calculations [15].…”

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

“…In [62], Muriki et al present the first portable, cost-effective, open source solution of RC-BLAST to guarantee usability. Kasap et al [52] also present a portable FPGA accelerator for BLAST by capturing the design with an FPGA-platformindependent language Handel-C.…”

The Research on BLAST Accelerator with Parallel Multi-Seeds Detection and Extension

“…活的算法适应性和较低的硬件代价成为理想的算法加速平台。为了提高搜索效率，基于 FPGA 平台的并 行 BLAST 算法成为研究热点。 近年来备受关注的研究成果有 Mercury BLASTn [9]- [11]、 Mercury BLASTp [12]、RC-BLAST [13]、Tree-BLAST [14]、FPGA/FLASH [15]、Multi-engine BLASTn [16] …”