Comparative RNA structure prediction beyond stochastic context free grammars

RNA分子是任何细胞中许多基本过程的核心。它们编码细胞中要合成的蛋白质组的信息;它们帮助合成蛋白质;它们控制蛋白质的生产速率（参见2006年诺贝尔医学奖）;它们也作为基因（所谓的RNA基因）。RNA分子是由四种基本结构单元组成的长度可变的线性链，核苷酸分别表示为A、C、G和U。RNA结构由RNA序列中非连续核苷酸对之间的弱氢键定义;三种可能的对是{A，U}，{G，C}和{G，U}。RNA序列可以呈现的可能的RNA结构的数量随着序列的长度呈指数增长。理论科学家面临的挑战是挑选出赋予RNA分子功能特性的RNA结构。为了解决这一挑战，大多数现有方法都依赖于RNA分子呈现最稳定结构的假设。最近的研究结果表明，这种假设一般不成立。我们建议开发新的，显着改进的，理论方法，不依赖于这个假设，并克服了现有方法的主要概念限制，以提高RNA结构预测，RNA基因预测，并解决许多最基本的和令人兴奋的问题，在分子生物学今天。

RNA molecules are at the core of numerous fundamental processes in any cell. They encode information on the set of proteins to be synthesized in a cell; they help synthesize proteins; they control protein-production rates (see Nobel Prize in Medicine 2006); and they also act as genes in their own right (so-called RNA genes). Many of these functions rely on the structure of the RNA molecule.RNA molecules are linear chains of variable lengths made of four elementary building blocks, the nucleotides denoted A, C, G and U. An RNA structure is defined by weak hydrogen bonds between pairs of non-consecutive nucleotides in the RNA sequence; the three possible pairs are {A, U}, {G, C} and {G, U}. The number of possible RNA structures that an RNA sequence can assume grows exponentially with the length of the sequence. The challenge to the theoretical scientist is to single out the RNA structure that confers the functional property to the RNA molecule.To address this challenge, most existing methods rely on the assumption that RNA molecules assume the most stable structure. Recent results show that this assumption does not hold in general. We propose to develop novel,significantly improved, theoretical methods which do not rely on this assumption and which overcome the major conceptual limitations of the existing methods in order to improve RNA structure prediction, RNA gene prediction and to address many of the most fundamental and exciting questions in molecular biology today.