Massively Parallel Solutions for Molecular Sequence Analysis
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
FPL '02 Proceedings of the Reconfigurable Computing Is Going Mainstream, 12th International Conference on Field-Programmable Logic and Applications
DASH: Localising Dynamic Programming for Order of Magnitude Faster, Accurate Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
DASH: Localising Dynamic Programming for Order of Magnitude Faster, Accurate Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Biosequence Similarity Search on the Mercury System
Journal of VLSI Signal Processing Systems
Acceleration of ungapped extension in Mercury BLAST
Microprocessors & Microsystems
Protein similarity search with subset seeds on a dedicated reconfigurable hardware
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
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We describe a novel hardware architecture for genomic and proteomic sequence alignment which achieves a speed-up of two to three orders of magnitude over Smith-Waterman dynamic programming (DP) in hardware [1]-[7]. In [8, 9] we introduce several features of our search algorithm, DASH, which outperforms NCBI-Blast (BLAST) [10] by an order of magnitude in software, and has better sensitivity. Indeed, DASH has been shown to have excellent sensitivity compared to Smith-Waterman. It is designed around the principle of considering genomic and proteomic sequence alignments to typically consist of regions of high homology (the diagonals) interspersed with regions of low homology. In DASH, the optimal solution consists of such diagonals joined by regions of exact DP. This is affordable due to the small area of these inter-connecting regions, Accordingly, we have designed a chip which finds the diagonals and performs the inter-region DP directly in hardware. On a Xilinx Virtex II, XC2V6000, FPGA, it performs over 10^12 base comparisons/second.