MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
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DOI：
10.1093/molbev/mst141
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发表时间：
2013-11
影响因子：
10.7
通讯作者：
Nishida M
中科院分区：
文献类型：
--
作者：
Iwasaki W;Fukunaga T;Isagozawa R;Yamada K;Maeda Y;Satoh TP;Sado T;Mabuchi K;Takeshima H;Miya M;Nishida M
Mitofish是一个鱼类线粒体基因组（mitogenomes）的数据库，包括强大而精确的从头注释的mitogenome序列。鱼类在脊椎动物进化和水圈生态学中占有重要地位，有丝分裂基因组序列数据已成为解决鱼类遗传问题和鉴定新鱼类物种的丰富信息来源。随着新的测序技术的出现，大量的有丝分裂基因组数据产生，有丝分裂基因组数据库的重要性继续快速增长。一个严重的瓶颈似乎可能会发生与有丝分裂基因组注释，因为压倒性的速度的数据积累和内在的困难，在注释序列与退化的转移RNA结构，不同的起始/终止密码子的编码元件，和相邻元件的重叠。为了缓解数据积压，我们开发了一个名为MitoAnnotator的注释管道。MitoAnnotator在大约5分钟内以高准确度自动注释鱼类有丝分裂基因组;因此，它很容易适用于数十个序列的数据集。MitoFish还包含先前测序的鱼类有丝分裂基因组的重新注释，使研究人员能够在发现注释可能错误或进行比较有丝分裂基因组分析时参考它们。对于需要更多关于鱼类分类、栖息地、表型或生命周期信息的用户，MitoFish提供了相关数据库的链接。MitoFish和MitoAnnotator可以在http://mitofish.aori.u-tokyo.ac.jp/上免费获得（最后一次访问是2013年8月28日）;所有数据都可以批量下载，注释管道可以通过Web界面使用。
Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface.
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影响因子：
3.9
作者：
OSAWA, S;OHAMA, T;WATANABE, K
通讯作者：
WATANABE, K
影响因子：
5.8
作者：
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作者：
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影响因子：
14.9
作者：
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通讯作者：
Stadler PF
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5.8
作者：
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通讯作者：
Canback, Bjorn