Linear-Time Algorithms for the Multiple Gene Duplication Problems

Author

Luo, Cheng-Wei ; Chen, Ming-Chiang ; Chen, Yi-Ching ; Yang, Roger W L ; Liu, Hsiao-Fei ; Chao, Kun-Mao

Author_Institution

Dept. of Comput. Sci. & Inf. Eng., Nat. Taiwan Univ., Taipei, Taiwan

Volume

8

Issue

1

fYear

2011

Firstpage

260

Lastpage

265

Abstract

A fundamental problem arising in the evolutionary molecular biology is to discover the locations of gene duplications and multiple gene duplication episodes based on the phylogenetic information. The solutions to the MULTIPLE GENE DUPLICATION problems can provide useful clues to place the gene duplication events onto the locations of a species tree and to expose the multiple gene duplication episodes. In this paper, we study two variations of the MULTIPLE GENE DUPLICATION problems: the EPISODE-CLUSTERING (EC) problem and the MINIMUM EPISODES (ME) problem. For the EC problem, we improve the results of Burleigh et al. with an optimal linear-time algorithm. For the ME problem, on the basis of the algorithm presented by Bansal and Eulenstein, we propose an optimal linear-time algorithm.

Keywords

bioinformatics; evolution (biological); genetics; molecular biophysics; EPISODE-CLUSTERING problem; MINIMUM EPISODES problem; evolutionary molecular biology; linear time algorithm; multiple gene duplication problem; phylogenetic information; Algorithm design and analysis; Bioinformatics; Biology computing; Biomedical engineering; Chaos; Computer science; Evolution (biology); Genomics; Organisms; Phylogeny; Computational phylogenetics; computations on discrete structures; gene duplication; linear-time algorithm.; Algorithms; Cluster Analysis; Computational Biology; Evolution, Molecular; Gene Duplication; Linear Models; Models, Genetic; Phylogeny;

fLanguage

English

Journal_Title

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Publisher

ieee

ISSN

1545-5963

Type

jour

DOI

10.1109/TCBB.2009.52

Filename

4967571