Journal of Jilin University(Engineering and Technology Edition) ›› 2018, Vol. 48 ›› Issue (5): 1593-1599.doi: 10.13229/j.cnki.jdxbgxb20170668

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Metagenomic clustering method based on k-mer frequency optimization

LIU Fu1,2, LAN Xu-teng1,2, HOU Tao2, KANG Bing2, LIU Yun2, LIN Cai-xia3   

  1. 1.State Key Laboratory of Automotive Simulation and Control,Jilin University,Changchun 130022,China;
    2.College of Communication Engineering, Jilin University, Changchun 130022, China;
    3.College of Information Science &Technology, Hainan University, Haikou 570228, China;
  • Received:2017-06-27 Online:2018-09-20 Published:2018-12-11

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Abstract: DNA sequence classification is a very important step in metagenomic study, and k-mer frequency is a commonly used feature for DNA sequence classification. The dimension of k-mer grows exponentially with k, easily leading to the “dimension disaster”. To solve this problem, this paper proposes a k-mer optimization based metagenomic DNA sequence classification method. First, the k-mer frequency is extracted for each DNA sequence. Second, the k-mer frequency is optimized based on Non-negative Matrix Factorization (NMF) algorithm. Finally, the fuzzy C-means clustering algorithm is used for DNA sequence clustering. Experimental results on metagenomic datasets containing different species show that the proposed method can effectively overcome the shortcoming of traditional classification method, and the classification performance is better than that of several similar algorithms.

Key words: computer application, pattern recognition and intelligent systems, k-mer, non-negative matrix factorization(NMF), fuzzy C-means method, metagenome

CLC Number: 

  • TP391
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