KnotAli: Informed Energy Minimization Through the Use of Evolutionary Information

Abstract

BackgroundImproving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a family to predict the structure. However, their prediction is limited to the consensus structure, and the quality of the alignment. Minimum free energy (MFE) based methods, on the other hand, do not rely on familial information and can predict structures of novel RNA molecules. Their prediction normally suffers from inaccuracies due to their underlying energy parameters. ResultsWe present a new method for prediction of RNA pseudoknotted secondary structures that combines the strengths of MFE prediction and alignment-based methods. KnotAli takes a multiple RNA sequence alignment and uses covariation and thermodynamic energy minimization to predict secondary structures for each individual sequence in the alignment. We compared KnotAli’s performance to that of three other alignment-based programs, on a large data set of 10 families with pseudoknotted and pseudoknot-free reference structures. We produced sequence alignments for each family using two well-known sequence aligners (MUSCLE and MAFFT). We found KnotAli to be superior in 6 of the 10 families for MUSCLE and 7 of the 10 for MAFFT. ConclusionsWe find KnotAli’s predictions to be less dependent on alignment quality. In particular, KnotAli is shown to have more accurate predictions compared to other leading methods as alignment quality deteriorates. KnotAli can be found online on github at https://github.com/mateog4712/KnotAli

Pseudoknots in RNA Structure Prediction

“…CaCoFold takes a set of pre‐aligned RNA sequences as input and uses probabilistic folding methods and positive and negative covariation scores to find a consensus structure. A recent method, KnotAli (Gray, Chester, & Jabbari, 2022), combines the strengths of thermodynamic‐based structure prediction and alignment‐based methods to accurately predict possibly pseudoknotted secondary structures for each individual sequence. It takes a set of previously aligned RNA sequences as input and uses covariation and thermodynamic energy minimization to predict possibly pseudoknotted secondary structures for each individual sequence in the alignment .…”