High Performance Biosequence Database Scanning using FPGAs

@article{Benkrid2007HighPB,
  title={High Performance Biosequence Database Scanning using FPGAs},
  author={Khaled Benkrid and Ying Liu and Abdsamad Benkrid},
  journal={2007 IEEE International Conference on Acoustics, Speech and Signal Processing - ICASSP '07},
  year={2007},
  volume={1},
  pages={I-361-I-364}
}
This paper presents the design and implementation of a generic and highly parameterised FPGA-based core for pairwise biological sequence alignment. The core is captured in the Handel-C language, which allows for high level software-like descriptions of hardware architectures. It implements the sequence alignment algorithm in hand using a pipeline of basic processing elements. This results in high performance FPGA implementations tailored to the algorithm in hand. For instance, actual hardware… CONTINUE READING