Exhaustive prediction of microRNAs, snoRNAs and their targets

以下是该项目的主要成果。(A)我们开发了一个microRNA查找工具，它结合了microRNA的结构和进化特征。我们表明，我们的工具比以前的方法性能更好，误报更少。(B)我们提出了一个计算RNA序列二级结构可及性的算法。我们能够检测到microRNAs靶点周围的进化制约因素。(C)我们开发了一个工具来计算RNA二级结构的自由能和熵随突变的变化。我们将我们的方法应用于线粒体tRNA，发现突变引起的结构波动增加与疾病易感性有关。(D)我们开发了一种工具来预测RNA序列每个碱基的潜在二级结构上下文。我们将我们的方法应用于RNA结合蛋白的结合部位，并检测了蛋白质的结构特异性。

The following is the main results of this project. (a) We developed a microRNA finding tool, which combines structural and evolutionary features of microRNAs. We showed that our tool outperforms previous methods with less false positives. (b) We developed an algorithm for computing secondary structural accessibilities of RNA sequences. We were able to detect the evolutionary constraints around the target sites of microRNAs. (c) We developed a tool to calculate the changes of free energies and entropies of RNA secondary structures in response to mutations. We applied our method to mitochondrial tRNAs and showed that the increase of structural fluctuation caused by mutations correlated with disease susceptibility. (d) We developed a tool to predict potential secondary structural contexts for each base of an RNA sequence. We applied our method to binding sites of RNA-binding proteins and detected the structural specificities of the proteins.