DNA multiple alignment problem with the new DiaWay algorithm

Abstract

DiaWay is a new efficient and robust algorithm of Multiple as well as pairwise DNA alignment, it is an improvement and re-implementation of the well known DIALIGN approach. In this paper we present the different steps of our approach, from the diagonals extraction and indexation step, to the gathering of the fragments and gaps insertion step, passing through the sorting of the consistent diagonals set for the final alignment. We present two implementations of our approach, the first one called DiaWay 1.0, and the second one called DiaWay 2.0. The results of tests and analysis performed on benchmarks taken from BAliBASE and smart databases show the effectiveness and efficiency of our approach, comparing to DIALIGN 2.2 algorithm in term of execution time.