Gene order alignment on trees with multiOrthoAlign.

Billel Benzaid,Nadia El-Mabrouk

doi:10.1186/1471-2164-15-s6-s5

Abstract

We relate the comparison of gene orders to an alignment problem. Our evolutionary model accounts for both rearrangement and content-modifying events. We present a heuristic based on dynamic programming for the inference of the median of three genomes and apply it in a phylogenetic framework. multiOrthoAlign is shown accurate on simulated and real datasets, and shown to significantly improve the running-time of DupLoCut, an "almost" exact algorithm based on linear programming, developed recently for the same problem.

Highlights

A major requirement in comparative genomics is to be able to compare genomes based on their whole content
Most of them are based on first identifying, in a pair-wise alignment dotplot, local alignments with high similarity score, and chaining them in a way maximizing an alignment score
DupLoCut is an “almost” exact heuristic based on linear programming

Summary

Introduction

A major requirement in comparative genomics is to be able to compare genomes based on their whole content. This is necessary for a myriad of applications such as phylogenetic reconstruction, orthology and paralogy identification, ancestral reconstruction and the study of evolutionary events. A large variety of algorithms have been developed for the comparison of wholegenome sequences with partial or no information on gene annotation. A recently developed method does not require any preliminary information on gene families [6], most of them assume a full or partial annotation of genomes, or a previously established large coverage of genomes in terms of syntenic blocks. Given two genomes represented as ordered sequences of genes (or building blocks), the rearrangement approach consists

Methods

Results

Conclusion