Alignment free characterization of the influenza-A hemagglutinin genes by the ISSCOR method

被引：2

作者：

Radomski, Jan P. ^{[1
]}

Slonimski, Piotr P. ^{[2
]}

机构：

[1] Warsaw Univ, Interdisciplinary Ctr Math & Computat Modeling, PL-02106 Warsaw, Poland

[2] Univ Paris 06, CNRS, Ctr Genet Mol, F-91190 Gif Sur Yvette, France

来源：

COMPTES RENDUS BIOLOGIES | 2012年 / 335卷 / 03期

关键词：

Alignment-free analysis; Random codon shuffling; Sequential order of synonymous codons; Synonymous codon replacement; Influenza virus; Hemagglutinin; Antigenic distance; Antigenic map; SURVEILLANCE SURVEILLANCE DATA; AMINO-ACID SUBSTITUTIONS; SYNONYMOUS CODON USAGE; H5N1; EVOLUTION; VIRUSES; SWINE; BIAS; VACCINE; REASSORTMENT;

D O I：

10.1016/j.crvi.2012.01.001

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Analyses and visualizations by the ISSCOR method of the influenza virus hemagglutinin genes of three different A-subtypes revealed some rather striking temporal (for A/H3N3), and spatial relationships (for A/H5N1) between groups of individual gene subsets. The application to the A/H1N1 set revealed also relationships between the seasonal H1, and the swine-like novel 2009 H1 v variants in a quick and unambiguous manner. Based on these examples we consider the application of the ISSCOR method for analysis of large sets of homologous genes as a worthwhile addition to a toolbox of genomics-it allows a rapid diagnostics of trends, and possibly can even aid an early warning of newly emerging epidemiological threats. (C) 2012 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

引用

页码：180 / 193

页数：14

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