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JCB
2000
129views more  JCB 2000»
13 years 4 months ago
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers
We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The p...
Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
ITNG
2006
IEEE
13 years 11 months ago
Evaluating Parallel Computing Systems in Bioinformatics
The utilization of parallel processing in bioinformatics is a relatively new development, and wide spread use of parallel processing in this domain has been limited by the availab...
Erik S. Gough, Michael D. Kane
ICDE
2011
IEEE
234views Database» more  ICDE 2011»
12 years 8 months ago
Massively parallel XML twig filtering using dynamic programming on FPGAs
Abstract— In recent years, XML-based Publish-Subscribe Systems have become popular due to the increased demand of timely event-notification. Users (or subscribers) pose complex ...
Roger Moussalli, Mariam Salloum, Walid A. Najjar, ...
ICSM
2007
IEEE
13 years 11 months ago
A Maintainable Software Architecture for Fast and Modular Bioinformatics Sequence Search
Bioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolu...
Jeremy S. Archuleta, Eli Tilevich, Wu-chun Feng
PPOPP
2012
ACM
12 years 18 days ago
Massively parallel breadth first search using a tree-structured memory model
Analysis of massive graphs has emerged as an important area for massively parallel computation. In this paper, it is shown how the Fresh Breeze trees-of-chunks memory model may be...
Tom St. John, Jack B. Dennis, Guang R. Gao