RNA Secondary Structure Analysis Using RNAstructure
Sara E. Ali, Abhinav Mittal, David H. Mathews- Medical Laboratory Technology
- Health Informatics
- General Pharmacology, Toxicology and Pharmaceutics
- General Immunology and Microbiology
- General Biochemistry, Genetics and Molecular Biology
- General Neuroscience
Abstract
RNAstructure is a user‐friendly program for the prediction and analysis of RNA secondary structure. It is available as a web server, a program with a graphical user interface, or a set of command line tools. The programs are available for Microsoft Windows, macOS, or Linux. This article provides protocols for prediction of RNA secondary structure (using the web server, the graphical user interface, or the command line) and high‐affinity oligonucleotide binding sites to a structured RNA target (using the graphical user interface). © 2023 Wiley Periodicals LLC.
Basic Protocol 1: Predicting RNA secondary structure using the RNAstructure web server
Alternate Protocol 1: Predicting secondary structure and base pair probabilities using the RNAstructure graphical user interface
Alternate Protocol 2: Predicting secondary structure and base pair probabilities using the RNAstructure command line interface
Basic Protocol 2: Predicting binding affinities of oligonucleotides complementary to an RNA target using OligoWalk