RNALogo: a new approach to display structural RNA alignment
RNALogo: a new approach to display structural RNA alignment
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DOI：
10.1093/nar/gkn258
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发表时间：
2008-07-01
影响因子：
14.9
通讯作者：
Huang, Hsien-Da
中科院分区：
文献类型：
--
作者：
Chang, Tzu-Hao;Horng, Jorng-Tzong;Huang, Hsien-Da
调控rna在许多重要的生物过程中发挥着重要作用，从基因调控到蛋白质合成。这项工作提出了一个基于网络的工具RNALogo，用于创建具有共识结构的多RNA序列比对模式的新图形表示。RNALogo图可以显示RNA序列比对及其一致的RNA二级结构中的重要特征。RNALogo扩展了序列标识，并将RNA二级结构和碱基配对区域的相互信息纳入图形表示中。每个RNALogo图由字母堆叠组成，在共识RNA二级结构中的每个位置都有一个堆叠。RNALogo提供了一个方便和高度可配置的标志生成器。RNALogo为Rfam中的每个RNA家族生成一个RNALogo图，这些生成的徽标被累积到RNALogo图库中。用户可以在这个图库中搜索或浏览RNALogo图，以获得已知RNA家族的其他视角。RNALogo现在可在：http://rnalogo.mbc.nctu.edu.tw/。
Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation. Each RNALogo graph is composed of stacks of letters, with one stack for each position in the consensus RNA secondary structure. RNALogo provides a convenient and high configurable logo generator. An RNALogo graph is generated for each RNA family in Rfam, and these generated logos are accumulated into a gallery of RNALogo. Users can search or browse RNALogo graphs in this gallery to receive additional perspectives of known RNA families. RNALogo is now available at: http://rnalogo.mbc.nctu.edu.tw/.