Schultz Jörg, Wolf Matthias
Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
Mol Phylogenet Evol. 2009 Aug;52(2):520-3. doi: 10.1016/j.ympev.2009.01.008.
The information that can be obtained from the secondary structure of the nuclear ribosomal internal transcribed spacer 2 (ITS2) is substantial, and yet many studies exploit this information inconsistently or inappropriately. This review introduces a remedy in the form of a flowchart where we detail the steps involved in estimating structure-based phylogenetic trees from ITS2 data. The pipeline described consists of the ITS2 Database, 4SALE, the CBCAnalyzer, and ProfDistS. Based on these tools, we describe how to utilize ITS2 sequence and secondary structure information together with an ITS2 specific scoring matrix and an ITS2 specific substitution model. The phylogenetic results thus obtained have been shown to be more reliable than approaches based on primary sequence data alone. Moreover, compensatory base changes (CBCs) in ITS2 sequence-structure pairs are identified as a possible marker for distinguishing species.
从核糖体内部转录间隔区2（ITS2）二级结构中可获取的信息非常丰富，但许多研究对这些信息的利用并不一致或并不恰当。本综述介绍了一种以流程图形式呈现的补救方法，我们在其中详细阐述了从ITS2数据估计基于结构的系统发育树所涉及的步骤。所描述的流程包括ITS2数据库、4SALE、CBCAnalyzer和ProfDistS。基于这些工具，我们描述了如何将ITS2序列和二级结构信息与ITS2特定评分矩阵和ITS2特定替代模型一起使用。如此获得的系统发育结果已被证明比仅基于一级序列数据的方法更可靠。此外，ITS2序列 - 结构对中的补偿性碱基变化（CBCs）被确定为区分物种的一种可能标记。
