Research on Phylogenetic Analysis and Feature Selection Based on HBV Sequence

Abstract

Abstract:

Hepatitis B Virus（HBV）infection is a global health problem and each HBV genotype has its unique feature. 10 patients
HBV sequences are used to study the evolutionary relationship and the process of mutation base of HBV on the sequence level.
Molecular Evolutionary Genetics Analysis（MEGA）software is firstly applied to make multiple sequence alignment and phylogenetic
analysis for HBV sequences. Then, Waikato Environment for Knowledge Analysis（WEKA）software is applied to conduct feature
selection for HBV sequence. The results show that the phylogenetic trees can accurately predict genotypes of 7 patients HBV
sequences. Furthermore, feature selection can improve the accuracy of classifiers.

Key words: HBV, multiple sequence alignment, phylogenetic analysis, feature selection

CLC Number:

R318.04

Xie Zuoxiang, Chen Xia, Zhang Junpeng*. Research on Phylogenetic Analysis and Feature Selection Based on HBV Sequence[J]. J4, 2015, 14(12): 43-46.

References

〔1〕World Health Organization. 乙型肝炎实况报道第204 号
〔EB/OL〕.〔2015-07-19〕. http：//www. who. int/mediacentre/
factsheets/fs204/zh/.
〔2〕BRECHOT C，POURCEL C，LOUISE A，et al. Presence of
integrated hepatitis B virus DNA sequences in cellular
DNA of human hepatocellular carcinoma〔J〕. Nature，1980，
286（5772）：533-535.
〔3〕SHEN T，GAO J，ZOU Y L，et al. Novel hepatitis B virus
sub genotype in the southern Yunnan Province of China〔J〕.
Intervirology，2009，52（6）：340-346.
〔4〕SAITOU N，NEI M. The neighbor-joining method：a new
method for reconstructing phylogenetic trees〔J〕. Molecular
Biology and Evolution，1987，4（4）：406-425.
〔5〕YANG Z. PAML：a program package for phylogenetic analy?
sis by maximum likelihood〔J〕. Computer Applications in
the Biosciences：CABIOS，1997，13（5）：555-556.
〔6〕RZHETSKY A，NEI M. A simple method for estimating and
testing minimum-evolution trees〔J〕. Mol Biol Evol，1992，
9（5）：945-967.
〔7〕TAKEZAKI N，NEI M. Genetic distances and reconstruc?
tion of phylogenetic trees from microsatellite DNA〔J〕.
Genetics，1996，144（1）：389-399.

〔8〕SAITOU N，IMANISHI T. Relative efficiencies of the Fitch-
Margoliash，maximum- parsimony，maximum- likelihood，
minimum-evolution，and neighbor-joining methods of phy?
logenetic tree construction in obtaining the correct tree〔J〕.
Mol Biol Evol，1989，6（5）：514-525.
〔9〕HALL M A. Correlation-based feature selection for ma?
chine learning〔D〕. Hamilton：The University of Waikato，
1999.
〔10〕YATES F. Contingency tables involving small numbers
and the χ2 test〔J〕. Supplement to the Journal of the Royal
Statistical Society，1934，1（2）：217-235.
〔11〕KULLBACK S，LEIBLER R A. On information and suffi?
ciency〔J〕. The Annals of Mathematical Statistics，1951，22
（1）：79-86.
〔12〕QUINLAN J R. C4. 5：programs for machine learning〔M〕.
Amsterdam：Elsevier，2014.
〔13〕RISHI.AnempiricalstudyofthenaiveBayesclassifier〔C〕/
IJCAI 2001 workshop on empirical methods in artificial
intelligence. 2001，3（22）：41-46.
〔14〕CORTES C，VAPNIK V. Support- vector networks〔J〕.
Machine Learning，1995，20（3）：273-297.
〔15〕BREIMAN L. Random forests〔J〕. Machine Learning，
2001，45（1）：5-32.
〔16〕GUYON I，ELISSEEFF A. An introduction to variable
and feature selection〔J〕. The Journal of Machine Learn?
ing Research，2003，3：1157-1182.
〔17〕AHMADIAN A，GHARIZADEH B，GUSTAFSSON A C，
et al. Single-nucleotide polymorphism analysis by pyrose?
quencing〔J〕. Analytical Biochemistry，2000，280（1）：103-
110.

[1]	. Clinical Diagnosis and Pathological Characteristics of Occult Hepatitis B [J]. Journal of Dali University, 2018, 3(2): 38-41.
[2]	Li Ze, Liu Jizheng, Shen Yuanying. Survey of Hepatitis B Immunization and Serological Markers of HBV in Dali [J]. J4, 2015, 14(10): 13-16.
[3]	LIN Mu, JIANG Xi-chao, SHEN Yuan-ying. Analysis of HBV Infection Risk Factors of the Khitan Descendants of Baoshan in Yunnan [J]. J4, 2014, 13(10): 47-50.