MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.
MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.
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DOI：
10.1093/dnares/dsn027
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发表时间：
2008-12
期刊：
影响因子：
4.1
通讯作者：
Itoh, Takehiko
中科院分区：
文献类型：
--
作者：
Noguchi, Hideki;Taniguchi, Takeaki;Itoh, Takehiko
DNA测序仪的最新进展正在加速基因组测序，特别是在微生物方面，来自不同物种的完整和草稿基因组已经被快速连续测序。在这里，我们提出了一个全面的基因预测工具，MetaGeneAnnotator(MGA)，它从单个或一组不同长度的匿名基因组序列中精确地预测各种原核基因。除了细菌和古生菌基因的统计模型外，MGA还集成了原噬菌体基因的统计模型，并使用来自输入序列的自我训练模型进行预测。因此，MGA不仅可以灵敏地检测典型基因，还可以检测非典型基因，例如原核生物基因组中的水平转移基因和原噬菌体基因。在本文中，我们还提出了一种新的分析核糖体结合位点(RBS)的方法，使我们能够检测RBSS的物种特异性模式。MGA基于这种方法建立了巧妙的RBS模型，并精确地预测了基因的翻译开始。通过使用适应的RBS模型，MGA还成功地提高了对短序列的预测精度(对于700bp片段，灵敏度为96%，特异度为93%)。MGA的这些特点加速了广泛的微生物基因组研究，如基因组注释和元基因组分析。
Recent advances in DNA sequencers are accelerating genome sequencing, especially in microbes, and complete and draft genomes from various species have been sequenced in rapid succession. Here, we present a comprehensive gene prediction tool, the MetaGeneAnnotator (MGA), which precisely predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths. The MGA integrates statistical models of prophage genes, in addition to those of bacterial and archaeal genes, and also uses a self-training model from input sequences for predictions. As a result, the MGA sensitively detects not only typical genes but also atypical genes, such as horizontally transferred and prophage genes in a prokaryotic genome. In this paper, we also propose a novel approach for analyzing the ribosomal binding site (RBS), which enables us to detect species-specific patterns of the RBSs. The MGA has the ingenious RBS model based on this approach, and precisely predicts translation starts of genes. The MGA also succeeds in improving prediction accuracies for short sequences by using the adapted RBS models (96% sensitivity and 93% specificity for 700 bp fragments). These features of the MGA expedite wide ranges of microbial genome studies, such as genome annotations and metagenome analyses.
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