Evolutionary two-dimensional DNA sequence alignment

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 pair-wise and multiple sequence alignment efficiently using genetic algorithms. © Springer-Verlag Berlin Heidelberg 2003.