《生命科学》 2014, 26(3): 219-227

非编码RNA的生物信息学研究方法：RNA结构预测及其应用

张浩文，杨禹丞，鲁　志^*

(清华大学生命科学学院生物信息学教育部重点实验室，北京 100084)

摘　要：近10 多年来的研究逐步揭示了RNA 的各种生物学功能。RNA 不仅是信息从DNA 传递到蛋白质的中间体，还直接参与基因沉默、表观遗传学修饰等生物学过程。单链的RNA 在体内通过碱基配对折叠成一定的二级结构。介绍了现在预测RNA 二级结构的主要算法及其应用，其中包括基于热力学、同源比对和统计学习的各种算法，以及如何引入实验数据辅助预测。二级结构预测算法被广泛用于寻找RNA功能单元和预测新非编码RNA等各种问题。如何利用高通量实验数据帮助结构预测，探索长非编码RNA功能，研究RNA 与蛋白质相互作用，是RNA 二级结构预测算法和应用的一些前沿方向。

From sequence to structure: RNA secondary structure prediction methods and the applications

ZHANG Hao-Wen， YANG Yu-Cheng， LU Zhi^*

(MOE Key Laboratory of Bioinformatics， School of Life Sciences， Tsinghua University， Beijing 100084， China)

Abstract: Researches in past 10 years uncovered various biological functions of RNA. Besides as the intermediate to transfer information from DNA to protein， RNA has been shown involved in gene silencing， epigenetic modifications and many other processes. RNAs are transcribed as single strand， fold into secondary structures bybase pairing. Here different algorithms of RNA secondary structure prediction and their applications are reviewed， including thermodynamic algorithms， homologous alignments comparison， statistical learning and incorporating experimental data into prediction model. RNA secondary structure prediction algorithms are widely used in detection of RNA functional elements， identification of new non-coding RNAs and other researches. Challenges such as determination of secondary structures transcriptome wide under the help of high-throughput sequencing，assist to long non-coding RNA function discoveries and study of protein-RNA interactions will draw more attentions in this field.