tRNAfinder: A Software System To Find All tRNA Genes in the DNA Sequence Based on the Cloverleaf Secondary Structure
tRNAfinder: A Software System To Find All tRNA Genes in the DNA Sequence Based on the Cloverleaf Secondary Structure
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DOI：
10.2751/jcac.7.116
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发表时间：
2006-01-01
影响因子：
--
通讯作者：
Kurokawa, Ken
中科院分区：
文献类型：
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作者：
Kinouchi, Makoto;Kurokawa, Ken
超过250个细菌基因组序列已被完全确定。这使得研究涉及多种生物体转录和翻译的物种特异性基因表达系统成为可能。要了解物种特异性翻译系统，了解单个物种的整套 tRNA 非常重要。当我们能够理解单个物种的整套 tRNA 时，我们可以根据 tRNA 水平和单个物种密码子使用的多变量分析来估计单个物种的最佳密码子，因为 tRNA 含量与基因组中同工 tRNA 基因的拷贝数之间存在高度相关性。因此，基因组中同受体 tRNA 的拷贝数对于理解物种特异性翻译系统非常重要。在本研究中，我们根据 DNA 序列开发了新的 tRNA 识别包，称为 tRNAfinder。检测tRNA的流程如下：首先，根据tRNA三叶草二级结构检测tRNA候选物。其次，根据源自真实 tRNA 的共识规则从候选者中选择 tRNA。在本研究中，我们通过使用 72 种伽马变形菌比较公开网站的 tRNA 组成来说明 tRNAfinder 算法和本系统的性能。此外，我们还研究了 γ 变形菌中 tRNA 组成的通用系统。本研究中开发的程序可以从我们的网站下载。
Over 250 bacterial genome sequences have been completely determined. This makes it possible to study the species-specific gene expression systems involving transcription and translation for a wide range of organisms. To understand species-specific translation system, it is important to comprehend the whole set of tRNAs for individual species. When we could comprehend the whole set of tRNAs for individual speices, we could estimate optimal codons for individual species based on levels of tRNAs and multivariate analysis of codon usage for individual species because of the high correlation between tRNA contents and copy numbers of isoaccepting tRNA genes in genomes. Thus, the copy numbers of isoaccepting tRNAs in genomes are very important for understanding species-specific translation system. In the present study, we developed new identification package of tRNAs from a DNA sequence called tRNAfinder. The procedure for detecting tRNAs are as follows: Firstly, tRNA candidates are detected based on tRNA cloverleaf secondary structure. Secondly, tRNAs are selected from the candidates based on the consensus rules derived from real tRNAs. In the present study we illustrate tRNAfinder algorithm and the performance of the present system by comparing composition of tRNAs from publicly available web sites using 72 gamma-proteobacteria. Furthermore we examine the universal system of tRNA composition in gamma proteobacteria. The programs developed in the present study are downloadable from our web site.