The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
Trees, stars, and multiple biological sequence alignment
SIAM Journal on Applied Mathematics
Adaptation in natural and artificial systems
Adaptation in natural and artificial systems
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
The evolutionary computation approach to motif discovery in biological sequences
GECCO '05 Proceedings of the 7th annual workshop on Genetic and evolutionary computation
A hybrid genetic search for multiple sequence alignment
Proceedings of the 8th annual conference on Genetic and evolutionary computation
Regulatory Motif Discovery Using a Population Clustering Evolutionary Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ICARIS'06 Proceedings of the 5th international conference on Artificial Immune Systems
A new greedy randomised adaptive search procedure for multiple sequence alignment
International Journal of Bioinformatics Research and Applications
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In this paper we provide a brief review of current work in the area of multiple sequence alignment (MSA) for DNA and protein sequences using evolutionary computation (EC). We detail the strengths and weaknesses of EC techniques for MSA. In addition, we present two novel approaches for inferring MSA using genetic algorithms. Our first novel approach utilizes a GA to evolve an optimal guide tree in a progressive alignment algorithm and serves as an alternative to the more traditional heuristic techniques such as neighbor-joining. The second novel approach facilitates the optimization of a consensus sequence with a GA using a vertically scalable encoding scheme in which the number of iterations needed to find the optimal solution is approximately the same regardless the number of sequences being aligned. We compare both of our novel approaches to the popular progressive alignment program Clustal W. Experiments have confirmed that EC constitutes an attractive and promising alternative to traditional heuristic algorithms for MSA.