The Deletion-Insertion model applied to the genome rearrangement problem

Abstract

Abstract Permutations are frequently used in solving the genome rearrangement problem, whose goal is finding the shortest sequence of mutations transforming one genome into another. We introduce the Deletion-Insertion model (DI) to model small-scale mutations in species with linear chromosomes, such as humans. Applying one restriction to this model, we obtain the transposition model for genome rearrangement, which was shown to be NP-hard in [4]. We use combinatorial reasoning and permutation statistics to develop a polynomial-time algorithm to approximate the minimum number of transpositions required in the transposition model and to analyze the sharpness of several bounds on transpositions between genomes.