Linear-time algorithms for the multiple gene duplication problems.
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.
Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan. b89902079@ntu.edu.tw
Cheng-Wei
CW
Luo
Ming-Chiang
MC
Chen
Yi-Ching
YC
Chen
Roger W L
RW
Yang
Hsiao-Fei
HF
Liu
Kun-Mao
KM
Chao
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D020440:Gene Duplication; D016014:Linear Models; D008957:Models, Genetic; D010802:Phylogeny