Solving the Protein Threading Problem in Parallel

Authors:
Nicola Yanev;Rumen Andonov
Affiliations:
-;-
Venue:
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Year:
2003

Citing 0
Cited 3

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Protein Threading: From Mathematical Models to Parallel Implementations

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Optimal protein threading by cost-splitting

WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics

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Abstract

We propose a network flow formulation for protein threading and show its equivalence with the shortest path problem on a graph with a particular structure. The underlying Mixed Integer Programming (MIP) model proves to be very appropriate-huge real-life instances have been solved in a reasonable time by using only a Mixed Integer Optimizer. The properties of the MIP model allow decomposition of the main problem on a large number of subproblems (tasks). We show that a branch&bound alike algorithm can be efficiently applied to solving in parallel these tasks, which leads to a significant reduction in the total running time.