Detection of tRNA Genes with Introns from DNA Sequences

Abstract

With the progress of genome projects, a vast amount of nucleotide sequence data is now available, which 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 for comprehending the whole set of tRNAs for individual species. We have been developing a procedure for detecting tRNA genes from DNA sequences. The procedure consists of 2 stages. The first stage finds out cloverleaf secondary structures. The second stage tries to reduce the number of the candidates of the tRNA genes by various restrictions. Some of the tRNA genes in Archaea and Eukaryotes have introns. In the present study, we improve the procedure to find them out. We applied the improved procedure to the complete genome sequence of Aeropyrum pernix (GenBank Accession BA000002) which has tRNA genes with introns. We assumed that the lengths of introns are 8--200 bases, and found 53352 candidates of the tRNA genes in the first stage. In the second stage, we obtained 49 candidates, 17 of which had introns.