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BMCBI
2010
189views more  BMCBI 2010»
13 years 9 months ago
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Background: Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly probl...
Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh,...
PPOPP
1997
ACM
14 years 1 months ago
LoPC: Modeling Contention in Parallel Algorithms
Parallel algorithm designers need computational models that take first order system costs into account, but are also simple enough to use in practice. This paper introduces the L...
Matthew Frank, Anant Agarwal, Mary K. Vernon
IPPS
1996
IEEE
14 years 1 months ago
Practical Parallel Algorithms for Dynamic Data Redistribution, Median Finding, and Selection
A common statistical problem is that of nding the median element in a set of data. This paper presents a fastand portable parallel algorithm for nding the median given a set of el...
David A. Bader, Joseph JáJá
CSB
2005
IEEE
139views Bioinformatics» more  CSB 2005»
14 years 2 months ago
Using Parallel Algorithms for Searching Molecular Sequence Databases
This work presents the development of algorithms for approximate string matching using parallel methods. It intends to do the maximum of molecular sequences comparisons per unity ...
Carla Correa Tavares dos Reis, Rubem P. Mondaini
EUROPAR
2008
Springer
13 years 10 months ago
Deque-Free Work-Optimal Parallel STL Algorithms
This paper presents provable work-optimal parallelizations of STL (Standard Template Library) algorithms based on the workstealing technique. Unlike previous approaches where a deq...
Daouda Traoré, Jean-Louis Roch, Nicolas Mai...