Abstract:
This paper presents the design and implementation of a high performance FPGA-based core for BLAST sequence alignment with the two-hit method. BLAST with two-hit is a very...Show MoreMetadata
Abstract:
This paper presents the design and implementation of a high performance FPGA-based core for BLAST sequence alignment with the two-hit method. BLAST with two-hit is a very widely used heuristic biological sequence alignment algorithm, and this paper is the first reported FPGA implementation of it, to our knowledge. The architecture of our core is parameterized in terms of the sequence lengths, match scores, gap penalties, and cut-off and threshold values. It is composed of various blocks each of which performs one step of the algorithm in parallel with the others. This results in a high performance and efficient FPGA implementation, which outperforms equivalent software implementations by one order of magnitude or more. Real hardware implementations show that our core is 52 times faster than equivalent software implementations, on average. Furthermore, the core was captured in an FPGA-platform-independent language, namely the Handel-C language, to which no specific resource inference or placement constraints were applied. Hence, the same code can be easily ported to different FPGA families and architectures.
Date of Conference: 08-10 October 2008
Date Added to IEEE Xplore: 08 December 2008
ISBN Information:
Keywords assist with retrieval of results and provide a means to discovering other relevant content. Learn more.
- IEEE Keywords
- Index Terms
- Sequence Alignment ,
- Cut-off Value ,
- Steps Of Algorithm ,
- Heuristic Algorithm ,
- Software Implementation ,
- Alignment Algorithm ,
- Hardware Implementation ,
- Matching Score ,
- Biological Sequences ,
- Parallel Algorithm ,
- Gap Penalty ,
- Place Constraints ,
- DNA Sequencing ,
- Protein Sequences ,
- Sequence Database ,
- Local Alignment ,
- Extension Step ,
- Query Sequence ,
- Software Applications ,
- Position Weight Matrices ,
- Clock Cycles ,
- Shift Register ,
- Highest Total Score ,
- Residue Pairs ,
- Hardware Architecture ,
- Big Box ,
- Smith-Waterman Algorithm ,
- Word List ,
- Computational Biology
Keywords assist with retrieval of results and provide a means to discovering other relevant content. Learn more.
- IEEE Keywords
- Index Terms
- Sequence Alignment ,
- Cut-off Value ,
- Steps Of Algorithm ,
- Heuristic Algorithm ,
- Software Implementation ,
- Alignment Algorithm ,
- Hardware Implementation ,
- Matching Score ,
- Biological Sequences ,
- Parallel Algorithm ,
- Gap Penalty ,
- Place Constraints ,
- DNA Sequencing ,
- Protein Sequences ,
- Sequence Database ,
- Local Alignment ,
- Extension Step ,
- Query Sequence ,
- Software Applications ,
- Position Weight Matrices ,
- Clock Cycles ,
- Shift Register ,
- Highest Total Score ,
- Residue Pairs ,
- Hardware Architecture ,
- Big Box ,
- Smith-Waterman Algorithm ,
- Word List ,
- Computational Biology