Numerical recipes in C: the art of scientific computing
Numerical recipes in C: the art of scientific computing
Simulated annealing and Boltzmann machines: a stochastic approach to combinatorial optimization and neural computing
Numerical analysis: mathematics of scientific computing
Numerical analysis: mathematics of scientific computing
Parallel programming with MPI
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A Parallel Genetic Algorithm for Physical Mapping of Chromosomes
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
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Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity. Parallel Monte Carlo methods for a maximum likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a simulated Monte Carlo algorithm. A two-tier parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the simulated Monte Carlo algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a network of shared-memory symmetric multiprocessors (SMPs) are presented.