title: Computational analysis of RNA structures with chemical probing data.
abstract: RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.
authors: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.
authors: Ping
authors: P
authors: Ge
authors: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA. Electronic address: shzhang@eecs.ucf.edu.
authors: Shaojie
authors: S
authors: Zhang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA
keywords: RNA secondary structure; RNA tertiary structure; chemical probing; parallel sequencing