Linear-Time Algorithms for the Multiple Gene Duplication Problems

被引:15
|
作者
Luo, Cheng-Wei [1 ]
Chen, Ming-Chiang [1 ]
Chen, Yi-Ching [1 ]
Yang, Roger W. L. [1 ]
Liu, Hsiao-Fei [1 ]
Chao, Kun-Mao [2 ,3 ]
机构
[1] Natl Taiwan Univ, Dept Comp Sci & Informat Engn, Taipei 106, Taiwan
[2] Natl Taiwan Univ, Grad Inst Biomed Elect & Bioinformat, Dept Comp Sci & Informat Engn, Taipei 106, Taiwan
[3] Natl Taiwan Univ, Grad Inst Networking & Multimedia, Taipei 106, Taiwan
关键词
Computational phylogenetics; gene duplication; computations on discrete structures; linear-time algorithm; TREES;
D O I
10.1109/TCBB.2009.52
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:260 / 265
页数:6
相关论文
共 50 条
  • [1] Linear-Time Algorithms for Tree Root Problems
    Chang, Maw-Shang
    Ko, Ming-Tat
    Lu, Hsueh-I
    [J]. ALGORITHMICA, 2015, 71 (02) : 471 - 495
  • [2] Linear-time algorithms for tree root problems
    Chang, Maw-Shang
    Ko, Ming-Tat
    Lu, Hsueh-I
    [J]. ALGORITHM THEORY - SWAT 2006, PROCEEDINGS, 2006, 4059 : 411 - 422
  • [3] Linear-Time Algorithms for Tree Root Problems
    Maw-Shang Chang
    Ming-Tat Ko
    Hsueh-I Lu
    [J]. Algorithmica, 2015, 71 : 471 - 495
  • [4] LINEAR-TIME ALGORITHMS AND NP-COMPLETE PROBLEMS
    GRANDJEAN, E
    [J]. SIAM JOURNAL ON COMPUTING, 1994, 23 (03) : 573 - 597
  • [5] On linear-time deterministic algorithms for optimization problems in fixed dimension
    Chazelle, B
    Matousek, J
    [J]. JOURNAL OF ALGORITHMS-COGNITION INFORMATICS AND LOGIC, 1996, 21 (03): : 579 - 597
  • [6] LINEAR-TIME ALGORITHMS FOR SOME SEPARABLE QUADRATIC-PROGRAMMING PROBLEMS
    MEGIDDO, N
    TAMIR, A
    [J]. OPERATIONS RESEARCH LETTERS, 1993, 13 (04) : 203 - 211
  • [7] Linear-time algorithms for the Hamiltonian problems on distance-hereditary graphs
    Hung, RW
    Chang, MS
    [J]. THEORETICAL COMPUTER SCIENCE, 2005, 341 (1-3) : 411 - 440
  • [8] Linear-time algorithms for problems on planar graphs with fixed disk dimension
    Abu-Khzam, Faisal N.
    Langston, Michael A.
    [J]. INFORMATION PROCESSING LETTERS, 2007, 101 (01) : 36 - 40
  • [9] LINEAR-TIME ALGORITHMS FOR DOMINATORS AND OTHER PATH-EVALUATION PROBLEMS
    Buchsbaum, Adam L.
    Georgiadis, Loukas
    Kaplan, Haim
    Rogers, Anne
    Tarjan, Robert E.
    Westbrook, Jeffery R.
    [J]. SIAM JOURNAL ON COMPUTING, 2008, 38 (04) : 1533 - 1573
  • [10] LINEAR-TIME ALGORITHMS IN MEMORY HIERARCHIES
    REGAN, KW
    [J]. INFORMATION PROCESSING '94, VOL I: TECHNOLOGY AND FOUNDATIONS, 1994, 51 : 288 - 293