RNA secondary structure prediction

CLC Genomics Workbench uses a minimum free energy (MFE) approach to predict RNA secondary structure. Here, the stability of a given secondary structure is defined by the amount of free energy used (or released) by its formation. The more negative free energy a structure has, the more likely is its formation since more stored energy is released by the event.

Free energy contributions are considered additive, so the total free energy of a secondary structure can be calculated by adding the free energies of the individual structural elements. Hence, the task of the prediction algorithm is to find the secondary structure with the minimum free energy. As input to the algorithm empirical energy parameters are used. These parameters summarize the free energy contribution associated with a large number of structural elements. A detailed structure overview can be found in Bioinformatics explained: RNA structure prediction.

In CLC Genomics Workbench, structures are predicted by a modified version of Professor Michael Zukers well known algorithm [Zuker, 1989b] which is the algorithm behind a number of RNA-folding packages including MFOLD. Our algorithm is a dynamic programming algorithm for free energy minimization which includes free energy increments for coaxial stacking of stems when they are either adjacent or separated by a single mismatch. The thermodynamic energy parameters used are from Mfold version 3, see http://mfold.rna.albany.edu/?q=mfold/mfold-references.