simulfold simultaneously inferring rna structures including pseudoknots, alignments, and trees using a bayesian mcmc framework同时simulfold推断rna结构包括基因、比对,和树木使用获得贝叶斯模型框架.pdfVIP

SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework 1,2* ´ ´ 3,4,5 Irmtraud M. Meyer , Istvan Miklos 1 UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada, 2 Department of Computer Science, University of British Columbia, ´ ´ Vancouver, British Columbia, Canada, 3 Alfred Renyi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, Hungary, 4 Computer and Automation Research ¨ ¨ ´ Institute (MTA-SZTAKI), Hungarian Academy of Sciences, Budapest, Hungary, 5 eScience Regional Knowledge Centre, Eotvos Lorand University, Budapest, Hungary 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 pr