The ITS2 Database
The ITS2 Database
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DOI：
10.3791/3806
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发表时间：
2012-03-01
影响因子：
1.2
通讯作者：
Wolf, Matthias
中科院分区：
文献类型：
--
作者：
Merget, Benjamin;Koetschan, Christian;Wolf, Matthias
ITS 2作为系统发育标记已经有二十多年的历史。由于ITS 2的研究主要集中在非常可变的ITS 2序列上，因此将该标记仅限于低水平的遗传学。然而，ITS 2序列及其高度保守的二级结构的组合提高了系统发育分辨率（1），并允许在多个分类等级进行系统发育推断，包括物种界定（2-8）JTS 2数据库（9）呈现了来自NCBI GenBank（11）的内部转录间隔区2序列的详尽数据集，其被准确地重新注释（10）。在通过轮廓隐马尔可夫模型（Hidden Markov Models，HMRM）进行注释之后，预测每个序列的二级结构。首先，测试基于最小能量的折叠（12）（直接折叠）是否导致正确的四螺旋构象。如果不是这种情况，则通过同源建模预测结构（13）。在同源性建模中，已知的二级结构被转移到另一个ITS 2序列，其二级结构不能在直接折叠中正确折叠。ITS 2数据库不仅是存储和检索ITS 2序列结构的数据库。它还提供了几种工具来处理您自己的ITS 2序列，包括注释，结构预测，基序检测和组合序列结构信息的BLAST（14）搜索。此外，它集成了4SALE（15，16）和ProfDistS（17）的修剪版本，用于多序列-结构比对计算和邻居连接（18）树重建。它们共同构成了一个连贯的分析管道，从初始序列集到基于序列和二级结构的系统发育。简而言之，这个工作台将首次系统发育分析简化为只需点击几下鼠标，同时还为全面的大规模分析提供了工具和数据。
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution(1) and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation(2-8).The ITS2 Database(9) presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank(11) accurately reannotated(10). Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold(12) (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling(13). In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST(14) search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE(15,16) and ProfDistS(17) for multiple sequence-structure alignment calculation and Neighbor Joining(18) tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.