title: tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.
abstract: The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.
authors.affiliation: Graduate School of Science and Technology, Niigata University Niigata, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.affiliation: Nagahama Institute of Bio-Science and Technology, Nagahama Shiga, Japan.
authors.forename: Hachiro
authors.initials: H
authors.lastname: Inokuchi
authors.affiliation: Nagahama Institute of Bio-Science and Technology, Nagahama Shiga, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Yamada
authors.affiliation: Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Muto
authors.affiliation: Nagahama Institute of Bio-Science and Technology, Nagahama Shiga, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Iwasaki
authors.affiliation: Nagahama Institute of Bio-Science and Technology, Nagahama Shiga, Japan.
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
keywords: BLSOM; big data; database; metagenome; phylogenic maker; tRNA