TRNADB-CE 2011: TRNA gene database curated manually by experts

Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi

研究成果: Article

43 引用 (Scopus)

抄録

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 sequence group, therefore, can be used as phylogenetic markers to clarify the microbial community structure of an ecosystem. The updated tRNADB-CE provided functions, with which users can obtain the phylotype-specific markers (e.g. genus-specific markers) by themselves and clarify microbial community structures of ecosystems in detail. tRNADB-CE can be accessed freely at http://trna.nagahama-i-bio.ac.jp.

元の言語English
ジャーナルNucleic Acids Research
39
発行部数SUPPL. 1
DOI
出版物ステータスPublished - 2011 1

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Transfer RNA
Databases
Genes
Metagenome
Ecosystem
Genome
Chloroplast Genome
Medicago
Eukaryota
Oligonucleotides
Viruses
Research

ASJC Scopus subject areas

  • Genetics

これを引用

Abe, T., Ikemura, T., Sugahara, J., Kanai, A., Ohara, Y., Uehara, H., ... Inokuchi, H. (2011). TRNADB-CE 2011: TRNA gene database curated manually by experts. Nucleic Acids Research, 39(SUPPL. 1). https://doi.org/10.1093/nar/gkq1007

TRNADB-CE 2011 : TRNA gene database curated manually by experts. / Abe, Takashi; Ikemura, Toshimichi; Sugahara, Junichi; Kanai, Akio; Ohara, Yasuo; Uehara, Hiroshi; Kinouchi, Makoto; Kanaya, Shigehiko; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro.

:: Nucleic Acids Research, 巻 39, 番号 SUPPL. 1, 01.2011.

研究成果: Article

Abe, T, Ikemura, T, Sugahara, J, Kanai, A, Ohara, Y, Uehara, H, Kinouchi, M, Kanaya, S, Yamada, Y, Muto, A & Inokuchi, H 2011, 'TRNADB-CE 2011: TRNA gene database curated manually by experts', Nucleic Acids Research, 巻. 39, 番号 SUPPL. 1. https://doi.org/10.1093/nar/gkq1007
Abe, Takashi ; Ikemura, Toshimichi ; Sugahara, Junichi ; Kanai, Akio ; Ohara, Yasuo ; Uehara, Hiroshi ; Kinouchi, Makoto ; Kanaya, Shigehiko ; Yamada, Yuko ; Muto, Akira ; Inokuchi, Hachiro. / TRNADB-CE 2011 : TRNA gene database curated manually by experts. :: Nucleic Acids Research. 2011 ; 巻 39, 番号 SUPPL. 1.
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