Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM):: characterization of horizontally transferred genes with emphasis on the E. coli O157 genome
Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM):: characterization of horizontally transferred genes with emphasis on the E. coli O157 genome
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DOI：
10.1016/s0378-1119(01)00673-4
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发表时间：
2001-10-03
期刊：
影响因子：
3.5
通讯作者：
Ikemura, T
中科院分区：
文献类型：
--
作者：
Kanaya, S;Kinouchi, M;Ikemura, T
随着可用DNA序列数据量的增加，开发用于全面系统分析和比较各种基因组的蛋白质编码序列的物种特异性特征的工具变得越来越重要。在本研究中，我们使用了一种新的神经网络算法，自组织映射（SOM），有效地和全面地分析密码子使用在大约60,000个基因从29个细菌物种同时。该SOM使得能够以比主成分分析更高的分辨率分别对单个物种的基因进行聚类和可视化。SOM的组织结构可以用基因组G + C%和tRNA组成来解释。我们使用SOM来检测E. coli O 157基因组中含有“O 157-unique segments”（O-islands），表明SOM是鉴定水平转移基因的有力工具。(C)2001 Elsevier Science B. V.保留所有权利。
With increases in the amounts of available DNA sequence data, it has become increasingly important to develop tools for comprehensive systematic analysis and comparison of species-specific characteristics of protein-coding sequences for a wide variety of genomes. In the present study, we used a novel neural-network algorithm, a self-organizing map (SOM), to efficiently and comprehensively analyze codon usage in approximately 60,000 genes from 29 bacterial species simultaneously. This SOM makes it possible to cluster and visualize genes of individual species separately at a much higher resolution than can be obtained with principal component analysis. The organization of the SOM can be explained by the genome G + C% and tRNA compositions of the individual species. We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes. (C) 2001 Elsevier Science B.V. All rights reserved.