Yang Huanwang, Jossinet Fabrice, Leontis Neocles, Chen Li, Westbrook John, Berman Helen, Westhof Eric
Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854-8087, USA.
Nucleic Acids Res. 2003 Jul 1;31(13):3450-60. doi: 10.1093/nar/gkg529.
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/.
已经开发了三个程序来辅助RNA结构的分类和可视化。BPViewer提供了一个网络界面，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，能自动识别和分类由沃森-克里克、 hoogsteen和糖边缘这三条边缘的各种组合在核酸结构中形成的碱基对类型。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二维图的各个部分，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。由于在移动所选部分时RNA的所有部分（如螺旋和单链）都是动态链接的，因此可以使用RNAMLview快速重新格式化二维图。通过碱基对注释和二维图形显示，可以快速识别和分类RNA基序。对从NDB数据库中选择的41个独特结构进行了一项调查。给出了四种碱基A、G、U和C的组合中每条边缘和12个碱基对家族中每个家族出现的统计数据。该程序还允许通过使用先前为碱基对提出的符号约定来可视化碱基对相互作用。BPViewer和RNAview的网络服务器可在http://ndbserver.rutgers.edu/services/上获取。应用程序RNAMLview也可以从该网站下载。RNAview生成的二维图可在http://ndbserver.rutgers.edu/atlas/的核酸数据库（NDB）中获取RNA结构。
