SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

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Abstract
Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest. These methods are indispensable not only for elucidating the regulatory roles of known RNA transcripts, but also for predicting RNA genes. It has been notoriously difficult to devise them to make the best use of the available data and to predict high-quality RNA structures that may also contain pseudoknots. We introduce a novel theoretical framework for co-estimating an RNA secondary structure including pseudoknots, a multiple sequence alignment, and an evolutionary tree, given several RNA input sequences. We also present an implementation of the framework in a new computer program, called SimulFold, which employs a Bayesian Markov chain Monte Carlo method to sample from the joint posterior distribution of RNA structures, alignments, and trees. We use the new framework to predict RNA structures, and comprehensively evaluate the quality of our predictions by comparing our results to those of several other programs. We also present preliminary data that show SimulFold's potential as an alignment and phylogeny prediction method. SimulFold overcomes many conceptual limitations that current RNA structure prediction methods face, introduces several new theoretical techniques, and generates high-quality predictions of conserved RNA structures that may include pseudoknots. It is thus likely to have a strong impact, both on the field of RNA structure prediction and on a wide range of data analyses. Not only is the prediction of evolutionarily conserved RNA structures important for elucidating the potential functions of RNA sequences and the mechanisms by which these functions are exerted, but it also lies at the core of RNA gene prediction. To get an accurate prediction of the conserved RNA structure, we need a high-quality sequence alignment and an evolutionary tree relating several evolutionarily related sequences. These are two strong requirements that are typically difficult to fulfill unless the encoded RNA structure is already known. We present what is to our knowledge the first method that solves this chicken-and-egg problem by co-estimating all three quantities simultaneously. We show that our novel method, called SimulFold, can be successfully applied over a wide range of sequence similarities to detect conserved RNA structures, including those with pseudoknots. We also show its potential as an alignment and phylogeny prediction method. Our method overcomes several significant limitations of existing methods and has the potential to be used for a very diverse range of tasks.