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| Motif Discovery and Phylogenetic Analysis of Hepatitis B Virus Sequences |
| ZHANG Qi1, ZHANG Jun-peng1, GAO Jian-mei2, HE Jian-feng1, YAN Xin-min2, MA Lei1, LI Jiu-yong2 |
1. Kunming University of Science and Technology, Yunnan Province Kunming 650504, China;
2. Institute of Basic Medicine of the First People's Hospital of Yunnan Province, and Center of Clinical Molecular Biology,and Kunhua Affiliated Hospital of Kunming Medical College Yunnan Province Kunming 650032, China |
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Abstract Hepatitis B virus (HBV) infection is a severe global health problem. In recent years, mutations as an essential element in the HBV evolution have been extensively studied. However, the study of the conserved sequence for the evolution of HBV is still in its infancy. In this paper, we applied MEME (multiple EM for motif elicitation) algorithm for motif discovery and proposed a new metric CI (conserved index) to make phylogenetic analysis of HBV sequences. Our results indicate that MEME can efficiently discover multiple motifs from HBV sequences and the new measurement CI for the conservative of sequences can effectively help us to build the phylogenetic tree. Thus, we can get evolutionary relationship of HBV sequence through the phylogenetic tree.
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Received: 15 June 2016
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Corresponding Authors:
HE Jian-feng. E-mail: jfenghe@kmust.edu.cn
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[1] Luo KX. Hepatitis B: Basic biology and clinical science[M]. Beijing: People's Medical Publishing House, 2001.
[2] Ferrari C. Hepattis B virus immunopathogenesis[J]. Annual Review of Immunology, 1995, 13(1): 29-60 .
[3] Abel L, Dessein AJ. The impact of host genetics onsusceptibility to human infectious diseases[J]. Annual Review of Immunology, 1997, 9 : 509-516.
[4] Michael Dean, Mary Carrington, Stephen J. O'Brien. Balanced polymorphisrn selected by genetic versus infectious human disease[J]. Annual Review of Genomics and Human Genetics, 2002, 3: 263-292.
[5] Adrian V, Hill S. The immunogenetics of human infectious diseases[J]. Annual Review of Immunology, 1998,16: 593-617.
[6] Hill AV. Host genetics of infectious diseases old and new approaches converge[J]. Emerging Infectious Disease, 1998, 4:695-697.
[7] Hertz GZ, HartzelL GW III, Stormo CD. Identification of consensus patterns in unaligned DNA sequences known to be functionally related[J]. Computer Applications in the Biosciences, 1990, 6: 81-92.
[8] Lawrence CE, Reilly AA. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligped biopolymer sequences[J]. Proteins: Sructure,Function, and Bioinformatics, 1990,7:41-51.
[9] Lawrence CE, Altschul SF, Boguski MS, et al. Detecting subtle sequence signals: a Gibbs sampling strategy for mutiple alignment[J]. Science, 1993, 262(5131): 208-214.
[10] BaileyTL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers[J]. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994, 2: 28-36.
[11] BaileyTL, Elkan C. Unsupervised leaming of multiple motifs in biopolymers using expectation maximization[J]. Machine Learning, 1995, 21:51-80. |
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