Zuker M, Jacobson A B
Institute for Biomedical Computing, Washington University, St. Louis, Missouri 63110, USA.
RNA. 1998 Jun;4(6):669-79. doi: 10.1017/s1355838298980116.
A number of heuristic descriptors have been developed previously in conjunction with the mfold package that describe the propensity of individual bases to participate in base pairs and whether or not a predicted helix is "well-determined." They were developed for the "energy dot plot" output of mfold. Two descriptors, P-num and H-num, are used to measure the level of promiscuity in the association of any given nucleotide or helix with alternative complementary pairs. The third descriptor, S-num, measures the propensity of bases to be single-stranded. In the current work, we describe a series of programs that were developed in order to annotate individual structures with "well-definedness" information. We use color annotation to present the information. The programs can annotate PostScript files that are created by the mfold package or the PostScript secondary structure plots produced by the Weiser and Noller program XRNA (Weiser B, Noller HF, 1995, XRNA: Auto-interactive program for modeling RNA, The Center for Molecular Biology of RNA, Santa Cruz, California: University of California; Internet: ftp://fangio.ucsc.edu/pub/XRNA). In addition, these programs can annotate ss files that serve as input to XRNA. The annotation package can also handle structure comparison with a reference structure. This feature can be used to compare predicted structure with a phylogenetically deduced model, to compare two different predicted foldings, and to identify conformational changes that are predicted between wild-type and mutant RNAs. We provide several examples of application. Predicted structures of two RNase P RNAs were colored with P-num information and further annotated with comparative information. The comparative model of a 16S rRNA was annotated with P-num information from mfold and with base pair probabilities obtained from the Vienna RNA folding package. Further annotation adds comparisons with the optimal foldings obtained from mfold and the Vienna package, respectively. The results of all of these analyses are discussed in the context of the reliability of structure prediction.
先前已结合mfold软件包开发了许多启发式描述符，这些描述符描述了单个碱基参与碱基对的倾向以及预测的螺旋是否“确定良好”。它们是为mfold的“能量点图”输出而开发的。两个描述符P-num和H-num用于测量任何给定核苷酸或螺旋与替代互补对结合的混杂程度。第三个描述符S-num测量碱基单链化的倾向。在当前工作中，我们描述了一系列为用“确定良好性”信息注释单个结构而开发的程序。我们使用颜色注释来呈现信息。这些程序可以注释由mfold软件包创建的PostScript文件或由Weiser和Noller程序XRNA（Weiser B，Noller HF，1995年，XRNA：用于RNA建模的自动交互式程序，RNA分子生物学中心，加利福尼亚州圣克鲁斯：加利福尼亚大学；互联网：ftp://fangio.ucsc.edu/pub/XRNA）生成的PostScript二级结构图。此外，这些程序可以注释用作XRNA输入的ss文件。注释包还可以处理与参考结构的结构比较。此功能可用于将预测结构与系统发育推导模型进行比较，比较两个不同的预测折叠，并识别野生型和突变型RNA之间预测的构象变化。我们提供了几个应用示例。两个核糖核酸酶P RNA的预测结构用P-num信息进行了着色，并进一步用比较信息进行了注释。一个16S rRNA的比较模型用来自mfold的P-num信息和从维也纳RNA折叠软件包获得的碱基对概率进行了注释。进一步的注释分别增加了与从mfold和维也纳软件包获得的最佳折叠的比较。所有这些分析的结果在结构预测可靠性的背景下进行了讨论。
