tRNAfinder: A Software System To Find All tRNA Genes in the DNA Sequence Based on the Cloverleaf Secondary Structure

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.