A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions

Martin Bader,Mohamed I Abouelhoda,Enno Ohlebusch

doi:10.1186/1471-2105-9-516

Martin Bader, Mohamed I Abouelhoda + Show 1 more

Open Access

https://doi.org/10.1186/1471-2105-9-516

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Abstract

BackgroundDue to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a very challenging task. For the most simple distance measures (the breakpoint distance and the reversal distance), the problem is NP-hard even if one considers only three genomes.ResultsIn this paper, we present a new heuristic algorithm that directly constructs a phylogenetic tree w.r.t. the weighted reversal and transposition distance. Experimental results on previously published datasets show that constructing phylogenetic trees in this way results in better trees than constructing the trees w.r.t. the reversal distance, and recalculating the weight of the trees with the weighted reversal and transposition distance. An implementation of the algorithm can be obtained from the authors.ConclusionThe possibility of creating phylogenetic trees directly w.r.t. the weighted reversal and transposition distance results in biologically more realistic scenarios. Our algorithm can solve today's most challenging biological datasets in a reasonable amount of time.

Highlights

Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available
Since BPAnalysis is no longer state-of-the-art and software tools have improved ever since, we investigated whether it is worthwhile to create a tree according to the reversal distance, and to recalculate the weights of the edges using the weighted reversal and transposition distance
Experimental results Weighted reversal and transposition distance The best results for the Campanulaceae dataset were achieved by phylo-m and phylo-tm, except for the weight ratio 1:1, where phylo-m found a tree with weight 38, while phylo-tm only found a tree with weight 39, see Table 3

Summary

Introduction

Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. This phylogenetic reconstruction is a very challenging task. For the most simple distance measures (the breakpoint distance and the reversal distance), the problem is NP-hard even if one considers only three genomes. During evolution both local and global mutations of DNA molecules occur. A section of the genome is excised and inserted at a new position in the genome; this may or may not involve an inversion. We are able to tackle the problem of reconstructing the evolutionary history of genomes

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