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» A Massively Parallel Architecture for Bioinformatics
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IPPS
2007
IEEE
14 years 1 months ago
Software and Algorithms for Graph Queries on Multithreaded Architectures
Search-based graph queries, such as finding short paths and isomorphic subgraphs, are dominated by memory latency. If input graphs can be partitioned appropriately, large cluster...
Jonathan W. Berry, Bruce Hendrickson, Simon Kahan,...
MAM
2007
113views more  MAM 2007»
13 years 7 months ago
A reconfigurable computing framework for multi-scale cellular image processing
Cellular computing architectures represent an important class of computation that are characterized by simple processing elements, local interconnect and massive parallelism. Thes...
Reid B. Porter, Jan R. Frigo, Al Conti, Neal R. Ha...
ASAP
2008
IEEE
186views Hardware» more  ASAP 2008»
14 years 1 months ago
Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs
RNA structure prediction, or folding, is a computeintensive task that lies at the core of several search applications in bioinformatics. We begin to address the need for high-thro...
Arpith C. Jacob, Jeremy Buhler, Roger D. Chamberla...
IPPS
2007
IEEE
14 years 1 months ago
High Performance Database Searching with HMMer on FPGAs
1 Profile Hidden Markov Models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared...
Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
IISWC
2006
IEEE
14 years 1 months ago
Performance Analysis of Sequence Alignment Applications
— Recent advances in molecular biology have led to a continued growth in the biological information generated by the scientific community. Additionally, this area has become a m...
Friman Sánchez, Esther Salamí, Alex ...