Using reliability information to annotate RNA secondary structures
Using reliability information to annotate RNA secondary structures
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DOI：
10.1017/s1355838298980116
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发表时间：
1998-06-01
期刊：
影响因子：
4.5
通讯作者：
Jacobson, AB
中科院分区：
文献类型：
--
作者：
Zuker, M;Jacobson, AB
许多启发式的描述符已经开发出以前与mfold包，描述了个别碱基参与碱基对的倾向，以及是否预测的螺旋是“良好确定的”。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，用于测量任何给定的核苷酸或螺旋与替代互补对的关联中的混杂水平。第三个描述符，S-num，措施的倾向基地是单链的，在目前的工作中，我们描述了一系列的程序，开发，以注释个别结构与“明确”的信息。我们使用颜色标注来呈现信息。程序可以注释由mfold包创建的XRNA文件或由Weiser和Noller程序XRNA产生的XRNA二级结构图（Weiser B，Noller HF，1995，XRNA：用于建模RNA的自动交互程序，RNA分子生物学中心，圣克鲁斯，加州：加州大学;因特网：ftp：//fangio.ucsc.edu/pub/XRNA）。此外，这些程序可以注释作为XRNA输入的se文件。注释包还可以处理与参考结构的结构比较。这个功能可以用来比较预测的结构与遗传学推导的模型，比较两个不同的预测折叠，并确定野生型和突变体RNA.We之间预测的构象变化提供了几个应用程序的例子。两种RNase P RNA的预测结构用P-num信息着色，并进一步用比较信息注释。16 S rRNA的比较模型用来自mfold的P-num信息和从维也纳RNA折叠包获得的碱基对概率注释。进一步的注释增加了比较，从mfold和维也纳包装年龄，分别获得的最佳折叠所有这些分析的结果进行了讨论的结构预测的可靠性的背景下。
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 se 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 pack age, respectively The results of all of these analyses are discussed in the context of the reliability of structure prediction.