Sequence alignment algorithms for run-length-encoded strings

Abstract

A unified framework is applied to solving various sequence comparison problems for run-length encoded strings. All of these algorithms take O( min {mn′,m′n}) time and O( max {m,n}) space, for two strings of lengths m and n, with m′ and n′ runs, respectively. We assume the linear-gap model and make no assumption on the scoring matrices, which maximizes the applicability of these algorithms. The trace (i.e., the way to align two strings) of an optimal solution can also be recovered within the same time and space bounds. © 2008 Springer-Verlag Berlin Heidelberg.