TY - JOUR
T1 - TRNADB-CE 2011
T2 - TRNA gene database curated manually by experts
AU - Abe, Takashi
AU - Ikemura, Toshimichi
AU - Sugahara, Junichi
AU - Kanai, Akio
AU - Ohara, Yasuo
AU - Uehara, Hiroshi
AU - Kinouchi, Makoto
AU - Kanaya, Shigehiko
AU - Yamada, Yuko
AU - Muto, Akira
AU - Inokuchi, Hachiro
N1 - Funding Information:
Integrated Database Project and a Grant-in-Aid for Publication of Scientific Research Results from the Ministry of Education, Culture, Sports, Science and Technology, Japan. Funding for open access charge: Integrated Database Project from the Ministry of Education, Culture, Sports, Science and Technology, Japan.
PY - 2011/1
Y1 - 2011/1
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkq1007
DO - 10.1093/nar/gkq1007
M3 - Article
C2 - 21071414
AN - SCOPUS:78651274780
SN - 0305-1048
VL - 39
SP - D210-D213
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -