Multitasking on FPGA Coprocessors
FPL '00 Proceedings of the The Roadmap to Reconfigurable Computing, 10th International Workshop on Field-Programmable Logic and Applications
A Co-processor System with a Virtex FPGA for Evolutionary Computation
FPL '00 Proceedings of the The Roadmap to Reconfigurable Computing, 10th International Workshop on Field-Programmable Logic and Applications
Customizing Graphics Applications: Techniques and Programming Interface
FCCM '00 Proceedings of the 2000 IEEE Symposium on Field-Programmable Custom Computing Machines
High Speed GAML-based Phylogenetic Tree Reconstruction Using HW/SW Codesign
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Multiple Sequence Alignment Based on Dynamic Programming Using FPGA
IEICE - Transactions on Information and Systems
Exhaustive peptide searching using relations
BNCOD'07 Proceedings of the 24th British national conference on Databases
Dynamic data folding with parameterizable FPGA configurations
ACM Transactions on Design Automation of Electronic Systems (TODAES)
Accelerating motif discovery: motif matching on parallel hardware
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Multidimensional dynamic programming for homology search on distributed systems
Euro-Par'06 Proceedings of the 12th international conference on Parallel Processing
Efficient architecture and scheduling technique for pairwise sequence alignment
ACM SIGARCH Computer Architecture News
A parallel cooperative team of multiobjective evolutionary algorithms for motif discovery
The Journal of Supercomputing
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In this paper, we show a new approach for homology search based on run-time reconfiguration. In our approach, the search consists of two phases, and different circuits are configured on demand during the search to make up for the limited memory bandwidth of off-theshelf FPGA boards. Experiments with an off-the-shelf FPGA (Xilinx XCV2000E) board showed good results. The time for comparing a query sequence of 2,048elemen ts with a database sequence of 64 million elements by the Smith-Waterman algorithm is about 34 sec, which is about 330 times faster than a desktop computer with a 1GHz Pentium-III.