5.8S-28S rRNA interaction and HMM-based ITS2 annotation
5.8S-28S rRNA interaction and HMM-based ITS2 annotation
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DOI：
10.1016/j.gene.2008.10.012
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发表时间：
2009-02-01
期刊：
影响因子：
3.5
通讯作者：
Wolf, Matthias
中科院分区：
文献类型：
--
作者：
Keller, Alexander;Schleicher, Tina;Wolf, Matthias
核核糖体重复单位的内转录间隔区2（ITS 2）是最常用的系统发育标记之一。它是一个快速进化的基因座，这使得它适合于在低分类水平上的研究，而其二级结构是非常保守的。在更高的分类学水平上重建树木是可能的。然而，ITS 2的起始和结束位置的注释在研究之间存在显著差异。这是一个严重的缺点，因为通过标准从头折叠程序预测正确的二级结构需要准确鉴定所讨论的标记。此外，正确的结构对于基于个体结构特征的多序列比对是必不可少的。本研究描述了一个新的工具，划定和识别的ITS 2。它是基于隐马尔可夫模型（HMM）和验证注释通过比较保守的结构基序在5.8S/28 S rRNA区域。我们的方法能够在基因库中超过30000个缺乏开始和结束注释的条目中识别和界定ITS 2。此外，45 000 ITS 2序列与一个有疑问的注释进行了重新注释。ITS 2-DB使用基于同源性的方法进行结构预测，其中约有30 000个条目被重新注释。我们表明，该方法是能够正确地注释ITS 2小到58核苷酸贾第鞭毛虫和ITS 2大到1160核苷酸从人类。因此，我们的方法应该是一个有价值的指导在任何基于ITS 2的系统发育分析的第一步和关键的一步：正确序列的划定。可以将序列提交至以下网站以进行基于HMM的ITS 2描绘：http://its2.bioapps.biozentrum.uni-wuerzburg.de。(C)2008 Elsevier B. V.保留所有权利。
The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate for studies at low taxonomic levels, whereas its secondary structure is well conserved. and tree reconstructions are possible at higher taxonomic levels. However, annotation of start and end positions of the ITS2 differs markedly between studies. This is a severe shortcoming, as prediction of a correct secondary structure by standard ab initio folding programs requires accurate identification of the marker in question. Furthermore, the correct structure is essential for multiple sequence alignments based on individual structural features. The present study describes a new tool for the delimitation and identification of the ITS2. It is based on hidden Markov models (HMMs) and verifies annotations by comparison to a conserved structural motif in the 5.8S/28S rRNA regions. Our method was able to identify and delimit the ITS2 in more than 30000 entries lacking start and end annotations in GenBank. Furthermore, 45 000 ITS2 sequences with a questionable annotation were reannotated. Approximately 30 000 entries from the ITS2-DB, that uses a homology-based method for structure prediction, were re-annotated. We show that the method is able to correctly annotate an ITS2 as small as 58 nt from Giardia lamblia and an ITS2 as large as 1160 nt from humans. Thus, our method should be a valuable guide during the first and crucial step in any ITS2-based phylogenetic analysis: the delineation of the correct sequence. Sequences can be submitted to the following website for HMM-based ITS2 delineation: http://its2.bioapps.biozentrum.uni-wuerzburg.de. (C) 2008 Elsevier B.V. All rights reserved.