tRNADB-CE 2011: tRNA gene database curated manually by experts

We updated the tRNADB-CE by analyzing 939 complete and 1301 draft genomes of prokaryotes and eukaryotes, 171 complete virus genomes, 121 complete chloroplast genomes and approximately 230 million sequences obtained by metagenome analyses of 210 environmental samples. The 287 102 tRNA genes in total, and thus two times of the tRNA genes compiled previously, are compiled, in which sequence information, clover-leaf structure and results of sequence similarity and oligonucleotide-pattern search can be browsed. In order to pool collective knowledge with help from any experts in the tRNA research field, we included a column to which comments can be added on each tRNA gene. By compiling tRNAs of known prokaryotes with identical sequences, we found high phylogenetic preservation of tRNA sequences, especially at a phylum level. Furthermore, a large number of tRNAs obtained by metagenome analyses of environmental samples had sequences identical to those found in known prokaryotes. The identical...

• Type: Journal
• Year: 2011
• Where: NAR
• Authors: Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi
• Keywords: Chloroplast Genomes, Microbial Community Structure, NAR 2011, Virus Genomes