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Abstract

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. 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 2 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 2 RNaseP 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.

Keywords: Keywords: RNA secondary structure, RNA folding, mfold, energy dot plot, boxplot, base pair uncertainty

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Next: Introduction Up: Using Reliability Information to Previous: Using Reliability Information to
Michael Zuker
Institute for Biomedical Computing
Washington University in St. Louis
August 21 1998.