The equilibrium partition function and base pair binding probabilities for RNA secondary structure

Abstract

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a "box matrix" display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage. The results are illustrated for representative tRNA, 5S RNA, and self-replicating and self-splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.

Computational methods in noncoding RNA research

“…This structure probability P S can be used to extract other information. McCaskill [96] proposed a formula to compute the probability of any two nucleotides in different positions to be paired in a secondary structure. The probability of each base pair (i, j) in a molecule is given by:…”

RNA Secondary Structure Analysis Using RNAstructure

“…Two reviews are available that explain dynamic programming in detail (Eddy, 2004;. The partition function is also calculated with a dynamic programming algorithm (McCaskill, 1990). …”

Variations on RNA folding and alignment: lessons from Benasque

“…The corresponding recursions for the partition functions (Z i j , Z B i j , Z M i j , Z M1 i j ) are obtained by replacing minimum operations with sums and additions with multiplications [16]:…”

“…6 we derived the snoRNA pattern from the human U65 snoRNA. First, we compute a pair probability matrix using McCaskill's algorithm [16] (RNAfold -p). Due to the very low sequence conservation, we ignore most of the sequence information is discarded.…”