Lagrangian approaches for a class of matching problems in computational biology

Authors:
Nicola Yanev;Rumen Andonov;Philippe Veber;Stefan Balev
Affiliations:
University of Sofia, 5 J. Bouchier Str., 1126 Sofia, Bulgaria;IRISA, Campus de Beaulieu, 35042 Rennes, France;IRISA, Campus de Beaulieu, 35042 Rennes, France;LITIS, University of Le Havre, 25 rue P. Lebon BP 540, 76058 Le Havre, France
Venue:
Computers & Mathematics with Applications
Year:
2008

Citing 6
Cited 1

Integer and combinatorial optimization

Integer and combinatorial optimization
On the approximation of protein threading

Theoretical Computer Science - Special issue: Genome informatics
Integer programming models for computational biology problems

Journal of Computer Science and Technology - Special issue on bioinformatics
FROST: Revisited and Distributed

IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
Parallel divide and conquer approach for the protein threading problem: Research Articles

Concurrency and Computation: Practice & Experience - High Performance Computational Biology
Protein Threading: From Mathematical Models to Parallel Implementations

INFORMS Journal on Computing

An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem

WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics

Quantified Score

Hi-index	0.09

Visualization

Abstract

This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching problem. We give formal graph and integer programming models of the problem. After studying the properties of these models, we propose two kinds of Lagrangian relaxation for solving them. We present experimental results on real-life instances showing the efficiency of our approaches.