tRNADB-CE 2011: tRNA gene database curated manually by experts.
tRNADB-CE 2011: tRNA gene database curated manually by experts.
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DOI：
10.1093/nar/gkq1007
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Inokuchi H
中科院分区：
文献类型：
--
作者：
Abe T;Ikemura T;Sugahara J;Kanai A;Ohara Y;Uehara H;Kinouchi M;Kanaya S;Yamada Y;Muto A;Inokuchi H
我们通过分析原核生物和真核生物的939个完整和1301个草案基因组，171个完整的病毒基因组，121个完整的叶绿体基因组和210个环境样品的宏基因组分析获得的约2.3亿个序列，更新了tRNADB-CE。对287 102个tRNA基因进行了编辑，编辑后的tRNA基因数量是以前编辑的两倍，可以浏览到序列信息、三叶草结构、序列相似性和序列模式搜索结果。为了在tRNA研究领域专家的帮助下汇集集体知识，我们包括了一个专栏，可以在其中添加对每个tRNA基因的评论。通过编译已知的原核生物的tRNA相同的序列，我们发现高系统发育保存的tRNA序列，特别是在门的水平。此外，通过对环境样品的宏基因组分析获得的大量tRNA的序列与已知原核生物中发现的序列相同。因此，相同的序列组可以作为系统发育标记来阐明生态系统的微生物群落结构。更新后的tRNADB-CE提供的功能，用户可以获得的微生物类型特异性标记（如属特异性标记），并阐明生态系统的微生物群落结构的细节。tRNADB-CE可在http://trna.nagahama-i-bio.ac.jp上免费访问。
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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影响因子：
14.9
作者：
Abe T;Ikemura T;Ohara Y;Uehara H;Kinouchi M;Kanaya S;Yamada Y;Muto A;Inokuchi H
通讯作者：
Inokuchi H
影响因子：
10.7
作者：
Sugahara, Junichi;Kikuta, Kaoru;Kanai, Akio
通讯作者：
Kanai, Akio
影响因子：
5.8
作者：
Li, Weizhong;Godzik, Adam
通讯作者：
Godzik, Adam
影响因子：
14.9
作者：
Laslett, D;Canback, B
通讯作者：
Canback, B
影响因子：
--
作者：
Kinouchi, Makoto;Kurokawa, Ken
通讯作者：
Kurokawa, Ken