Abstract
Pseudo-energies are a generic method to incorporate extrinsic information into energy-directed RNA secondary structure predictions. Consensus structures of RNA families, usually predicted from multiple sequence alignments, can be treated as soft constraints in this manner. In this contribution we first revisit the theoretical framework and then show that pseudo-energies for the centroid base pairs of the consensus structure result in a substantial increase in folding accuracy. In contrast, only a moderate improvement can be achieved if only the information that a base is predominantly paired is utilized.
This work was funded by the Deutsche Forschungsgemeinschaft (DFG grant number STA 850/48-1) and by the Austrian Science Fund (FWF grant number F-80 and I-4520).
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von Löhneysen, S. et al. (2023). Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. In: Guo, X., Mangul, S., Patterson, M., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science(), vol 14248. Springer, Singapore. https://doi.org/10.1007/978-981-99-7074-2_21
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