ISSN 1000-1239 CN 11-1777/TP

Journal of Computer Research and Development ›› 2019, Vol. 56 ›› Issue (9): 1907-1917.doi: 10.7544/issn1000-1239.2019.20180835

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Design and Implementation of Pairwise Sequence Alignment Algorithm Components Based on Dynamic Programming

Shi Haihe, Zhou Weixing   

  1. (School of Computer and Information Engineering, Jiangxi Normal University, Nanchang 330022)
  • Online:2019-09-10
  • Supported by: 
    This work was supported by the National Natural Science Foundation of China (61662035, 61762049, 61862033).

Abstract: Pairwise sequence alignment algorithm is a key algorithm in bioinformatics, and it is widely used in sequence similarity analysis and genomic sequence database searching. The existing study mainly focuses on the optimization and use of relative alignment algorithms for specific application problems. To some extent, those studies lack a high-level algorithm framework that not only has led to the redundancy of the sequence alignment algorithms and the possible errors caused by the artificial selection algorithm, but also made the structure of algorithm difficult to be understood effectively. Through in-depth analysis of the dynamic programming-based pairwise sequence alignment algorithms domain(DPPSAA), a domain feature model and the corresponding algorithm component interactive model have been established, a DPPSAA component library has been formally implemented by the PAR platform, and a concrete algorithm has been assembled, thus the reliability of the algorithm for formal assembly is guaranteed, moreover a valuable reference for the application of sequence similarity analysis algorithms is provided. Finally, the C++ program generation system of PAR platform is used to transform the assembly alignment algorithm into C++ program and the running results show that the dynamic programming-based pairwise sequence alignment algorithm component library has certain practicability.

Key words: pairwise sequence alignment algorithm, dynamic programming, feature model, component interactive model, PAR platform

CLC Number: