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Evolutionary Two-Dimensional DNA Sequence Alignment
Edgar E. Vallejo1 and Fernando Ramos2
1Computer Science Dept.,
Tecnológico de Monterrey,
Campus Estado de México
Carretera Lago de Guadalupe Km 3.5
Col. Margarita Maza de Juárez,
52926Atizapán de Zaragoza,
Eestado de México, México
vallejo@itesm.mx
2Computer Science Dept.,
Tecnológico de Monterrey,
Campus Cuernavaca
Ave. Paseo de la Reforma 182
Col. Lomas de Cuernavaca, 62589
Cuernavaca, Morelos, México
fernando.ramos@itesm.mx
Abstract. This article presents a model for DNA sequence alignment. In our model, a finite state automaton writes two-dimensional maps of nucleotide sequences. An evolutionary method for sequence alignment from this representation is proposed. We use HIV as the working example. Experimental results indicate that structural similarities produced by two-dimensional representation of sequences allow us to perform pairwise and multiple sequence alignment efficiently using genetic algorithms.
LNCS 2723, p. 429 f.
lncs@springer.de
© Springer-Verlag Berlin Heidelberg 2003