An optimization approach to multiple sequence alignment

被引：0
|
作者：
Hunt, FY [1 ]
Kearsley, AJ
Wan, HH
机构：
[1] Natl Inst Stand & Technol, Math & Computat Sci Div, Gaithersburg, MD 20899 USA
[2] NIH, Natl Ctr Genome Res, Bethesda, MD 20894 USA
来源：
APPLIED MATHEMATICS LETTERS | 2003年 / 16卷 / 05期
关键词：
linear programming; sequencing; alignment;
D O I：
10.1016/S0893-9659(03)00083-1
中图分类号：
O29 [应用数学];
学科分类号：
070104 ;
摘要：
The problem of multiple sequence alignment is recast as an optimization problem using Markov decision theory. One seeks to minimize the expected or average cost of alignment subject to data-derived constraints. In this setting, the problem is equivalent to a linear program which can be solved efficiently using modern interior-point methods. We present numerical results from an implementation of the algorithm for protein sequence alignment. (C) 2003 Elsevier Science Ltd. All rights reserved.
引用
收藏
页码：785 / 790
页数：6
相关论文
共 50 条
  • [1] A Genetic Algorithm based Approach for the Optimization of Multiple Sequence Alignment
    Mishra, Arunima
    Tripathi, B. K.
    Soam, Sudhir Singh
    [J]. 2020 INTERNATIONAL CONFERENCE ON COMPUTATIONAL PERFORMANCE EVALUATION (COMPE-2020), 2020, : 415 - 418
  • [2] Optimization alignment: The end of multiple sequence alignment in phylogenetics?
    Wheeler, W
    [J]. CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY, 1996, 12 (01): : 1 - 9
  • [3] Optimization of multiple-sequence alignment based on multiple-structure alignment
    Shatsky, M
    Nussinov, R
    Wolfson, HJ
    [J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 62 (01) : 209 - 217
  • [4] Partitioned optimization algorithms for multiple sequence alignment
    Chen, Yixin
    Pan, Yi
    Chen, Juan
    Liu, Wei
    Chen, Ling
    [J]. 20TH INTERNATIONAL CONFERENCE ON ADVANCED INFORMATION NETWORKING AND APPLICATIONS, VOL 2, PROCEEDINGS, 2006, : 618 - +
  • [5] A time warping approach to multiple sequence alignment
    Arribas-Gil, Ana
    Matias, Catherine
    [J]. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, 2017, 16 (02) : 133 - 144
  • [6] An Evolutionary Approach for Performing Multiple Sequence Alignment
    Mateus Silva, Fernando Jose
    Manuel Sanchez-Perez, Juan
    Antonio Gomez-Pulido, Juan
    Vega-Rodriguez, Miguel A.
    [J]. 2010 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC), 2010,
  • [7] An Optimization Approach for Multiple Sequence Alignment using Divide-Conquer and Genetic Algorithm
    Mishra, Arunima
    Soam, Sudhir Singh
    Tripathi, Bipin Kumar
    [J]. INTERNATIONAL JOURNAL OF ADVANCED COMPUTER SCIENCE AND APPLICATIONS, 2021, 12 (04) : 453 - 458
  • [8] Ant colony optimization method for multiple sequence alignment
    Chen, Ling
    Liu, Wei
    Chen, Juan
    [J]. PROCEEDINGS OF 2007 INTERNATIONAL CONFERENCE ON MACHINE LEARNING AND CYBERNETICS, VOLS 1-7, 2007, : 914 - 919
  • [9] WOAMSA: Whale Optimization Algorithm for Multiple Sequence Alignment of Protein Sequence
    Kumar, Manish
    Kumar, Ranjeet
    Nidhya, R.
    [J]. COMPUTATIONAL VISION AND BIO-INSPIRED COMPUTING, 2020, 1108 : 131 - 139
  • [10] A novel two-level particle swarm optimization approach for efficient multiple sequence alignment
    Soniya Lalwani
    Rajesh Kumar
    Nilama Gupta
    [J]. Memetic Computing, 2015, 7 : 119 - 133
12345