A new genetic algorithm for multiple sequence alignment

Narimani, Z ; Sharif University of Technology | 2012

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  1. Type of Document: Article
  2. DOI: 10.1142/S146902681250023X
  3. Publisher: 2012
  4. Abstract:
  5. Multiple sequence alignment (MSA) is one of the basic and important problems in molecular biology. MSA can be used for different purposes including finding the conserved motifs and structurally important regions in protein sequences and determine evolutionary distance between sequences. Aligning several sequences cannot be done in polynomial time and therefore heuristic methods such as genetic algorithms can be used to find approximate solutions of MSA problems. Several algorithms based on genetic algorithms have been developed for this problem in recent years. Most of these algorithms use very complicated, problem specific and time consuming mutation operators. In this paper, we propose a new algorithm that uses a new way of population initialization and simple mutation and recombination operators. The strength of the proposed GA is using simple mutation operators and also a special recombination operator that does not have problems of similar recombination operators in other GAs. The experimental results show that the proposed algorithm is capable of finding good MSAs in contrast to existing methods, while it uses simple operators with low computational complexity
  6. Keywords:
  7. Fitness function ; Genetic algorithms ; Multiple sequence alignment ; Approximate solution ; Evolutionary distance ; Fitness functions ; Genetic operators ; Low computational complexity ; Multiple sequence alignments ; Mutation operators ; New genetic algorithms ; Polynomial-time ; Population initializations ; Protein sequences ; Recombination operators ; Heuristic methods ; Molecular biology ; Polynomial approximation ; Genetic algorithms
  8. Source: International Journal of Computational Intelligence and Applications ; Volume 11, Issue 4 , December , 2012 ; 14690268 (ISSN)
  9. URL: http://www.worldscientific.com/doi/abs/10.1142/S146902681250023X