title: Computational prediction of RNA secondary structure.
abstract: The purpose of this section is to detail methods for the computational prediction of RNA secondary structure. This protocol is intended to provide an easy entry into the field of RNA structure prediction for those wishing to utilize it in their research and to suggest 'best practices' for going from sequence to secondary structure depending on the available data.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, NY, USA. Electronic address: wmoss2@mail.rochester.edu.
authors.forename: Walter N
authors.initials: WN
authors.lastname: Moss
mesh_terms: D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D012984:Software
chemical_list: D012313:RNA
keywords: Basic Local Alignment Search Tool (BLAST); Dynalign; Minimum free energy (MFE) structure; Pseudoknots; RNAstructure; Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE); Watson–Crick base pairs