USING RELIABILITY INFORMATION TO ANNOTATE RNA SECONDARY STRUCTURES

A number of heuristic descriptors have been developed previously in co njunction with the mfold package that describe the propensity of indiv idual bases to participate in base pairs and whether or not a predicte d helix is ''well-determined.'' They were developed for the ''energy d ot 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 nu cleotide or helix with alternative complementary pairs. The third desc riptor, S-num, measures the propensity of bases to be single-stranded, In the current work, we describe a series of programs that were devel oped in order to annotate individual structures with ''well-definednes s'' information. We use color annotation to present the information. T he programs can annotate PostScript files that are created by the mfol d package or the PostScript secondary structure plots produced by the Weiser and Noller program XRNA (Weiser B, Noller HF, 1995, XRNA:Auto-i nteractive program for modeling RNA, The Center for Molecular Biology of RNA, Santa Cruz, California: University of California; Internet: ft p://fangio.ucsc.edu/pub/XRNA). In addition, these programs can annotat e se files that serve as input to XRNA. The annotation package can als o handle structure comparison with a reference structure. This feature can be used to compare predicted structure with a phylogenetically de duced model, to compare two different predicted foldings, and to ident ify conformational changes that are predicted between wild-type and mu tant RNAs. We provide several examples of application. Predicted struc tures of two RNase P RNAs were colored with P-num information and furt her annotated with comparative information. The comparative model of a 16S rRNA was annotated with P-num information from mfold and with bas e pair probabilities obtained from the Vienna RNA folding package. Fur ther annotation adds comparisons with the optimal foldings obtained fr om mfold and the Vienna pack age, respectively The results of all of t hese analyses are discussed in the context of the reliability of struc ture prediction.