We consider how the orthology/paralogy information can be corrected in order to represent a gene tree, a problem that has recently gained interest in phylogenomics. Interestingly, the problem is related to the Minimum CoGraph Editing problem on the relation graph that represents orthology/paralogy information, where we want to minimize the number of edit operations on the given relation graph in order to obtain a cograph. In this paper we provide both theoretical and experimental results on the Minimum CoGraph Editing problem. On the theoretical side, we provide approximation algorithms for bounded degree relation graphs, for the general problem and for the problem restricted to deletion of edges. On the experimental side, we present a genetic algorithm for Minimum CoGraph Editing and we provide an experimental evaluation of the genetic algorithm on synthetic data.

Dondi, R., Mauri, G., Zoppis, I. (2017). Orthology Correction for Gene Tree Reconstruction: Theoretical and Experimental Results. In Proc. ICCS 2017 – Int. Conf. on Computational Science (pp.1115-1124). Amsterdam : Elsevier B.V. [10.1016/j.procs.2017.05.047].

Orthology Correction for Gene Tree Reconstruction: Theoretical and Experimental Results

MAURI, GIANCARLO
Secondo
;
ZOPPIS, ITALO FRANCESCO
Ultimo
2017

Abstract

We consider how the orthology/paralogy information can be corrected in order to represent a gene tree, a problem that has recently gained interest in phylogenomics. Interestingly, the problem is related to the Minimum CoGraph Editing problem on the relation graph that represents orthology/paralogy information, where we want to minimize the number of edit operations on the given relation graph in order to obtain a cograph. In this paper we provide both theoretical and experimental results on the Minimum CoGraph Editing problem. On the theoretical side, we provide approximation algorithms for bounded degree relation graphs, for the general problem and for the problem restricted to deletion of edges. On the experimental side, we present a genetic algorithm for Minimum CoGraph Editing and we provide an experimental evaluation of the genetic algorithm on synthetic data.
slide + paper
Orthologous Genes, Gene Tree Reconstruction, CoGraph Editing, Approximation Algorithms, Genetic Algorithms
English
International Conference on Computational Science ICCS June 12-14
2017
Proc. ICCS 2017 – Int. Conf. on Computational Science
2017
108
1115
1124
partially_open
Dondi, R., Mauri, G., Zoppis, I. (2017). Orthology Correction for Gene Tree Reconstruction: Theoretical and Experimental Results. In Proc. ICCS 2017 – Int. Conf. on Computational Science (pp.1115-1124). Amsterdam : Elsevier B.V. [10.1016/j.procs.2017.05.047].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/162952
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