Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
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DOI：
10.1093/nar/gkz833
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发表时间：
2019-11-18
影响因子：
14.9
通讯作者：
Bernt, Matthias
中科院分区：
文献类型：
--
作者：
Donath, Alexander;Juehling, Frank;Bernt, Matthias
随着已测序的后生动物线粒体基因组的迅速增加，详细的人工注释变得越来越不可行。虽然很容易确定编码蛋白质的基因在有丝分裂基因组中的大致位置，但线粒体转录本的特殊处理使确定精确的基因边界成为一个令人惊讶的困难问题。我们详细分析了注释的起始密码子位置和终止密码子位置的性质，并利用推断的模式设计了一种新的方法来预测从头注释中的基因边界。我们的方法得益于经验观察到的起始/终止密码子和基因长度的普遍存在，并考虑了这些特征对遗传密码变化的依赖。虽然不是完美的，但我们的新方法在基因边界的准确性方面产生了巨大的改进，并将线粒体基因组注释服务器Mitos升级为一个更复杂的工具，用于全自动注释后生动物线粒体基因组。
With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.