An ant colony pairwise alignment based on the dot plots

Sequence alignment is one of the most important operations in bioinformatics. In this article, we introduced a new method for pairwise alignment. We associated the process of aligning with the plan by the modified dot plots. The next position will be selected by the number of pheromone and the matching score of the candidates. The presented algorithm can be used to find the best aligning result without calculating the scoring matrix. Superiority of the presented algorithm has been proved in several experiments. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009

[1]  Temple F. Smith,et al.  Comparison of biosequences , 1981 .

[2]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[3]  Christian Blum,et al.  An ant colony optimization algorithm for DNA sequencing by hybridization , 2008, Comput. Oper. Res..

[4]  Ling Zhang,et al.  Rapid and sensitive dot-matrix methods for genome analysis , 2004, Bioinform..

[5]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  Dejan Plavšić,et al.  A novel unexpected use of a graphical representation of DNA : Graphical alignment of DNA sequences , 2006 .

[8]  Lu Xu,et al.  A novel invariant and sequence comparison for DNA , 2007 .

[9]  M Dorigo,et al.  Ant colonies for the travelling salesman problem. , 1997, Bio Systems.

[10]  Nirupam Chakraborti,et al.  A novel method for alignment of two nucleic acid sequences using ant colony optimization and genetic algorithms , 2007, Appl. Soft Comput..

[11]  Zne-Jung Lee,et al.  Genetic algorithm with ant colony optimization (GA-ACO) for multiple sequence alignment , 2008, Appl. Soft Comput..

[12]  W. Miller,et al.  A time-efficient, linear-space local similarity algorithm , 1991 .

[13]  Milan Randić.  On a geometry-based approach to protein sequence alignment , 2008 .