Parallel sequence alignment algorithm for clustering system

被引：0
|
作者：
Chen, Yang [1 ]
Yu, Songnian [1 ]
Leng, Ming [1 ]
机构：
[1] Shanghai Univ, Sch Engn & Comp Sci, Shanghai, Peoples R China
来源：
KNOWLEDGE ENTERPRISE: INTELLIGENT STRATEGIES IN PRODUCT DESIGN, MANUFACTURING, AND MANAGEMENT | 2006年 / 207卷
关键词：
bioinformatics; sequence alignment; parallel algorithm; clustering system; MPI;
D O I：
暂无
中图分类号：
T [工业技术];
学科分类号：
08 ;
摘要：
Sequence alignment is one of the most important fundamental operations in bioinformatics. It has been successfully applied to predict the function, structure and evolution of biological sequences. In this paper, the sequence alignment algorithms based on dynamic programming are analyzed and compared. We present a parallel algorithm for pairwise alignment and implement it on a clustering system with MPI. The experimental results demonstrate the effectiveness in performance promotion. We encapsulate the algorithm into a grid service for practical use.
引用
收藏
页码：311 / +
页数：2
相关论文
共 50 条
  • [1] A Greedy Clustering Algorithm for Multiple Sequence Alignment
    Lebsir, Rabah
    Layeb, Abdesslem
    Fariza, Tahi
    INTERNATIONAL JOURNAL OF COGNITIVE INFORMATICS AND NATURAL INTELLIGENCE, 2021, 15 (04)
  • [2] A Parallel Pairwise Local Sequence Alignment Algorithm
    Bandyopadhyay, Sanghamitra
    Mitra, Ramkrishna
    IEEE TRANSACTIONS ON NANOBIOSCIENCE, 2009, 8 (02) : 139 - 146
  • [3] A parallel algorithm for the constrained multiple sequence alignment problem
    He, D
    Arslan, AN
    BIBE 2005: 5TH IEEE SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, 2005, : 258 - 262
  • [4] A Multigroup Parallel Genetic Algorithm for Multiple Sequence Alignment
    Luo, Jiawei
    Zhang, Li
    Liang, Cheng
    ARTIFICIAL INTELLIGENCE AND COMPUTATIONAL INTELLIGENCE, PT I, 2011, 7002 : 308 - 316
  • [5] Longest Sorted Sequence algorithm for parallel text alignment
    Ildefonso, T
    Lopes, GP
    COMPUTER AIDED SYSTEMS THEORY - EUROCAST 2005, 2005, 3643 : 81 - 90
  • [6] Multiple molecular sequence alignment by island parallel genetic algorithm
    Anbarasu, LA
    Narayanasamy, P
    Sundararajan, V
    CURRENT SCIENCE, 2000, 78 (07): : 858 - 863
  • [7] A one-phase parallel algorithm for the sequence alignment problem
    Lecroq, Thierry
    Myoupo, Jean-Frederic
    Seme, David
    Parallel Processing Letters, 1998, 8 (04): : 515 - 526
  • [8] A parallel hybrid genetic algorithm for multiple protein sequence alignment
    Nguyen, HD
    Yoshihara, I
    Yamamori, K
    Yasunaga, M
    CEC'02: PROCEEDINGS OF THE 2002 CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1 AND 2, 2002, : 309 - 314
  • [9] A Parallel Niched Pareto Evolutionary Algorithm for Multiple Sequence Alignment
    Mateus da Silva, Fernando Jose
    Sanchez Perez, Juan Manuel
    Gomez Pulido, Juan Antonio
    Vega Rodriguez, Miguel A.
    5TH INTERNATIONAL CONFERENCE ON PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY & BIOINFORMATICS (PACBB 2011), 2011, 93 : 157 - +
  • [10] A PARALLEL ALGORITHM FOR LARGE-SCALE MULTIPLE SEQUENCE ALIGNMENT
    Lopes, Heitor S.
    Erig Lima, Carlos R.
    Moritz, Guilherme L.
    COMPUTING AND INFORMATICS, 2010, 29 (06) : 1233 - 1250
12345