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NCBI BLASTP on High-Performance Reconfigurable Computing Systems
2015
ACM Transactions on Reconfigurable Technology and Systems
The BLAST sequence alignment program is a central application in Bioinformatics. The de facto standard version, NCBI BLAST, uses complex heuristics which make it challenging to simultaneously achieve both high performance and exact agreement. We propose a system that uses novel FPGA-based filters that reduce the input database by over 99.97% without loss of sensitivity. There are several contributions. First is design of the filters themselves, which perform two-hit seeding, exhaustive ungapped
doi:10.1145/2629691
fatcat:aqtru5wepbegvk4p6gapqgvi5q