The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
Annals of Operations Research - Special issue on Tabu search
Tabu Search
Design and Evaluation of Tabu Search Algorithms forMultiprocessor Scheduling
Journal of Heuristics
Cooperative Parallel Tabu Search for Capacitated Network Design
Journal of Heuristics
Protein Conformation of a Lattice Model Using Tabu Search
Journal of Global Optimization
An Efficient Algorithm for the Knapsack Sharing Problem
Computational Optimization and Applications
An overview of protein-folding techniques: issues and perspectives
International Journal of Bioinformatics Research and Applications
Multiple sequence alignment by quantum genetic algorithm
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
A quantum evolutionary algorithm for effective multiple sequence alignment
EPIA'05 Proceedings of the 12th Portuguese conference on Progress in Artificial Intelligence
A new greedy randomised adaptive search procedure for multiple sequence alignment
International Journal of Bioinformatics Research and Applications
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Tabu search is a meta-heuristic approach that is found to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to align multiple sequences. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification. It intensifies by bringing the search process to poorly aligned regions of an elite solution, and softly diversifies by moving from one poorly aligned region to another. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that for datasets comprising orphan sequences, divergent families and long internal insertions, tabu search generates better alignment as compared to other methods studied in this paper. The source code of our tabu search algorithm is available at http://www.bii.a-star.edu.sg/~tariq/tabu/.