Abstract
We describe the first algorithm and software, RNAenn, to compute the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model. Our next-nearest-neighbor triplet energy model appears to lead to somewhat more cooperative folding than does the nearest neighbor energy model, as judged by melting curves computed with RNAenn and with two popular software implementations for the nearest-neighbor energy model. A web server is available at http://bioinformatics.bc.edu/clotelab/RNAenn/.
Highlights
Thermodynamics-based ab initio RNA secondary structure algorithms are used to detect microRNAs [1], targets of microRNAs [2], non-coding RNA genes [3], temperaturedependent riboregulators [4], selenoproteins [5], ribosomal frameshift locations [6], RNA-protein binding sites [7], etc
RNA sequence a~a1, . . . ,an is a set of base pairs (i,j), 1ƒivjƒn, such that (1) ai,aj forms a Watson Crick AU, UA, GC, CG or wobble GU, UG pair; (2) each base is paired to at most one other base, i.e. (i,j),(i,k)[S implies that j~k, and (i,j),(k,j)[S implies that i~k; (3) there are no pseudoknots in S, where a pseudoknot consists of base pairs (i,j),(k,‘) where ivkvjv‘; (4) each hairpin loop has at least h unpaired bases; i.e. (i,j)[S implies that j{i§hz1
We have introduced a new energy model extended nearest neighbor (ENN) for RNA secondary structure prediction and implemented it in a tool called RNAenn along with new energy parameters for triplet stacking inferred using Brown’s algorithm
Summary
Thermodynamics-based ab initio RNA secondary structure algorithms are used to detect microRNAs [1], targets of microRNAs [2], non-coding RNA genes [3], temperaturedependent riboregulators [4], selenoproteins [5], ribosomal frameshift locations [6], RNA-protein binding sites [7], etc. The importance and ubiquity of RNA thermodynamics-based algorithms cannot be overemphasized – there are even applications in RNA design for novel cancer therapies and in synthetic biology. In [8] Vashishta et al used the RNA minimum free energy (MFE) structure prediction algorithm mfold [9] to design seven anti-pCD ribozymes, four of which were cloned, stably transfected in the highly metastatic human breast cancer cell line, MDA-MB231, and shown to have a therapeutic potential by knocking down the expression of pCD. Altman, are RNA enzymes that can cleave a molecule or catalyze a reaction.)
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