FROST: Revisited and Distributed
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
Parallel evolution strategy on grids for the protein threading problem
Journal of Parallel and Distributed Computing
Lagrangian approaches for a class of matching problems in computational biology
Computers & Mathematics with Applications
Optimal protein threading by cost-splitting
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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For the Protein Threading Problem (PTP) we propose a network-flow like formulation. We also show its equivalence with a generalization of the shortest path problem on a graph with a very particular structure. The underlying Mixed Integer Programming (MIP) model proves to be very appropriate for the PTP—large real-life instances have been solved much faster by using only the MIP solver CPLEX instead of a known special-purpose branch and bound algorithm. The properties of the MIP model permit a decomposition of the main problem into a large number of subproblems (tasks). We show that a branch and cut strategy can be efficiently applied for solving these tasks in a parallel manner, which leads to a significant reduction in the total running time. Computational experiments with large problem instances are presented. Copyright © 2004 John Wiley & Sons, Ltd.This work has been done when R. Andonov was on leave with IRISA/INRIA, Rennes