A new method for analyzing H5N1 avian influenza virus

被引：6

作者：

Liu, Yanqiu ^{[1
]}

Zhang, Yusen ^{[1
]}

机构：

[1] Shandong Univ, Sch Math & Stat, Weihai 264209, Peoples R China

来源：

JOURNAL OF MATHEMATICAL CHEMISTRY | 2010年 / 47卷 / 03期

关键词：

Amino acid; H5N1 avian influenza virus; Similarity matrix; Phylogenic tree; GRAPHICAL REPRESENTATION; HEMAGGLUTININ;

D O I：

10.1007/s10910-009-9641-2

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

In this paper a novel method for phylogenetic analysis of H5N1 avian influenza virus has been proposed. At first we provide a mapping of virus protein sequence. Based on this mapping, we propose a new distance measure and make use of the corresponding similarity matrix to construct phylogenic tree without requiring multiple alignment. As an application, we construct phylogenic tree for 123 species of H5N1 avian influenza virus. The phylogeny obtained is generally consistent with evolutionary trees constructed in previous studies.

引用

页码：1129 / 1144

页数：16

共 19 条

[1]

Aubin JT, 2005, EMERG INFECT DIS, V11, P1515

[2] Visualization and analysis of DNA sequences using DNA walks [J].

Berger, JA ;

Mitra, SK ;

Carli, M ;

Neri, A .

JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS, 2004, 341 (1-2) :37-53

[3] Characterization of a novel influenza a virus hemagglutinin subtype (H16) obtained from black-headed gulls [J].

Fouchier, RAM ;

Munster, V ;

Wallensten, A ;

Bestebroer, TM ;

Herfst, S ;

Smith, D ;

Rimmelzwaan, GF ;

Olsen, B ;

Osterhaus, ADME .

JOURNAL OF VIROLOGY, 2005, 79 (05) :2814-2822

[4] CombiMatrix oligonucleotide arrays:: Genotyping and gene expression assays employing electrochemical detection [J].

Ghindilis, Andrey L. ;

Smith, Maria W. ;

Schwarzkopf, Kevin R. ;

Roth, Kristian M. ;

Peyvan, Kia ;

Munro, Sandra B. ;

Lodes, Michael J. ;

Stover, Axel G. ;

Bernards, Karen ;

Dill, Kilian ;

McShea, Andy .

BIOSENSORS & BIOELECTRONICS, 2007, 22 (9-10) :1853-1860

[5] H5N1 influenza: A protean pandemic threat [J].

Guan, Y ;

Poon, LLM ;

Cheung, CY ;

Ellis, TM ;

Lim, W ;

Lipatov, AS ;

Chan, KH ;

Sturm-Ramirez, KM ;

Cheung, CL ;

Leung, YHC ;

Yuen, KY ;

Webster, RG ;

Peiris, JSM .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (21) :8156-8161

[6] Evolutionary characterization of the six internal genes of H5N1 human influenza A virus [J].

Hiromoto, Y ;

Yamazaki, Y ;

Fukushima, T ;

Saito, T ;

Lindstrom, SE ;

Omoe, K ;

Nerome, R ;

Lim, W ;

Sugita, S ;

Nerome, K .

JOURNAL OF GENERAL VIROLOGY, 2000, 81 :1293-1303

[7]

KILBOURNE ED, 2007, J INFECT DIS S1, V176, pS29

[8] Detection of Hong Kong 97-like H5N1 influenza viruses from eggs of Vietnamese waterfowl [J].

Li, Y. ;

Lin, Z. ;

Shi, J. ;

Qi, Q. ;

Deng, G. ;

Li, Z. ;

Wang, X. ;

Tian, G. ;

Chen, H. .

ARCHIVES OF VIROLOGY, 2006, 151 (08) :1615-1624

[9] Novel method for analyzing proteome [J].

Liao, Bo ;

Luo, Jiawei ;

Li, Renfa ;

Zhu, Wen .

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 2007, 107 (06) :1295-1300

[10] Unique graphical representation of protein sequences based on nucleotide triplet codons [J].

Randic, M ;

Zupan, J ;

Balaban, AT .

CHEMICAL PHYSICS LETTERS, 2004, 397 (1-3) :247-252

← 1 2 →