Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences
Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences
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DOI：
10.1093/oxfordjournals.molbev.a026048
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发表时间：
1999-10-01
影响因子：
10.7
通讯作者：
Fertil, B
中科院分区：
文献类型：
--
作者：
Deschavanne, PJ;Giron, A;Fertil, B
我们通过源自“混沌动力系统”理论（所谓的混沌游戏表示[CGR]）的新工具探索了基因组的DNA结构，该工具允许以图像的形式描述寡核苷酸的频率。使用 CGR，我们观察到基因组的子序列表现出整个基因组的主要特征，证明了基因组签名概念的有效性。碱基浓度、延伸（互补碱基或嘌呤/嘧啶的运行）和补丁（不同长度的过度或表达不足的单词）是解释序列之间观察到的变异性的主要因素。图像之间的距离可以被认为是系统发育接近度的度量。真核生物和原核生物只能根据它们的 DNA 结构来识别。
We explored DNA structures of genomes by means of a new tool derived from the "chaotic dynamical systems" theory (the so-called chaos game representation [CGR]), which allows the depiction of frequencies of oligonucleotides in the form of images. Using CGR, we observe that subsequences of a genome exhibit the main characteristics of the whole genome, attesting to the validity of the genomic signature concept. Base concentrations, stretches (runs of complementary bases or purines/pyrimidines), and patches (over- or underexpressed words of various lengths) are the main factors explaining the variability observed among sequences. The distance between images may be considered a measure of phylogenetic proximity. Eukaryotes and prokaryotes can be identified merely on the basis of their DNA structures.