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Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK.
Nucleic Acids Res. 2000 Oct 15;28(20):3839-45. doi: 10.1093/nar/28.20.3839.
Comparative analysis is the preferred method of inferring RNA secondary structure, but its use requires considerable expertise and manual effort. As the importance of secondary structure for accurate sequence alignment and phylogenetic analysis becomes increasingly realised, the need for secondary structure models for diverse taxonomic groups becomes more pressing. The number of available structures bears little relation to the relative diversity or importance of the different taxonomic groups. Insects, for example, comprise the largest group of animals and yet are very poorly represented in secondary structure databases. This paper explores the utility of maximum weighted matching (MWM) to help automate the process of comparative analysis by inferring secondary structure for insect mitochondrial small subunit (12S) rRNA sequences. By combining information on correlated changes in substitutions and helix dot plots, MWM can rapidly generate plausible models of secondary structure. These models can be further refined using standard comparative techniques. This paper presents a secondary structure model for insect 12S rRNA based on an alignment of 225 insect sequences and an alignment for 16 exemplar insect sequences. This alignment is used as a template for a web server that automatically generates secondary structures for insect sequences.
比较分析是推断RNA二级结构的首选方法，但其应用需要相当多的专业知识和人工操作。随着二级结构对于准确序列比对和系统发育分析的重要性越来越被认识到，为不同分类群构建二级结构模型的需求变得更加迫切。现有结构的数量与不同分类群的相对多样性或重要性几乎没有关系。例如，昆虫是最大的动物类群，但在二级结构数据库中的代表性却很差。本文探讨了最大加权匹配（MWM）的效用，通过推断昆虫线粒体小亚基（12S）rRNA序列的二级结构来帮助自动化比较分析过程。通过结合替换中的相关变化信息和螺旋点图，MWM可以快速生成合理的二级结构模型。这些模型可以使用标准的比较技术进一步优化。本文基于225条昆虫序列的比对以及16条典型昆虫序列的比对，提出了昆虫12S rRNA的二级结构模型。该比对被用作一个网络服务器的模板，该服务器可自动为昆虫序列生成二级结构。
