Tools for the automatic identification and classification of RNA base pairs
Tools for the automatic identification and classification of RNA base pairs
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DOI：
10.1093/nar/gkg529
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Westhof, E
中科院分区：
文献类型：
--
作者：
Yang, HW;Jossinet, F;Westhof, E
已经开发了三个程序来帮助RNA结构的分类和可视化。BPViewer提供了一个Web界面，用于显示单个碱基对或碱基对集合的三维（3D）坐标。一个网络服务器，RNAview，自动识别和分类的碱基对的类型形成的核酸结构的各种组合的三个边缘，沃森克里克，胡格斯汀和糖边缘。RNAView以Postscript、VRML或RNAML格式生成二级和三级结构的二维（2D）图。应用程序RNAMLview可用于重新排列RNAView 2D图的各个部分，以生成标准表示（如tRNA的三叶草结构）或用户所需的任何布局。一个2D图可以使用RNAMLview快速重新格式化，因为RNA的所有部分（如螺旋和单链）在移动选定部分时都是动态连接的。通过碱基对注释和二维图形显示，可以快速识别和分类RNA模体。对从NDB数据库中选出的41个独特结构进行了调查。对于四种碱基：A、G、U和C的组合，给出了每个边缘和每个12 bp家族的出现的统计。该程序还允许通过使用先前提出的碱基对的符号约定来可视化碱基对相互作用。BPViewer和RNAview的Web服务器位于http://ndbserver.rutgers.edu/services/。应用程序RNAMLview也可以从这个网站下载。RNAview生成的2D图可在核酸数据库（NDB）中获得，网址为http://ndbserver.rutgers.edu/atlas/。
Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.