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RNAborMEA computes a maximum expected accuracy analogue Z(δ) of the Boltzmann partition function, called the pseudo Boltzmann partition function, as well as the maximum expected accuracy structures MEA(δ) for a given RNA sequence. Here, a structure T is a δ-neighbor of a given structure S, if S can be transformed into T by a minimum number δ of edit operations, where an edit operation consists of removing or adding a single base pair (i.e. if the base pair distance between S and T is δ). Since it has been shown that the maximum expected accuracy structure is often closer to the native structure than is the minimum free energy structure, our work permits one to determine those structures which have maximum expected accuracy, when compared with all structural neighbors within distance δ. Better candidates for the difficult-to-predict gene-ON structure of purine riboswitches are found using RNAborMEA than all current software to generate suboptimal structures.

If you use RNAborMEA in your work, please consider citing the papers:
Peter Clote, Feng Lou, William A. Lorenz.
Maximum expected accuracy structural neighbors of an RNA secondary structure.
BMC Bioinformatics BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S.
Feng Lou and Peter Clote. Maximum expected accurate structural neighbors of an RNA secondary structure. Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Feb 3-5, 2011, 123-128, Orlando, FL, ISBN 978-1-61284-851-8, doi 10.1109/ICCABS.2011.5729865.