Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences

Yukiteru Ono; Kiyoshi Asai

doi:10.1007/978-1-0716-2768-6_1

Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences

Methods Mol Biol. 2023:2586:1-14. doi: 10.1007/978-1-0716-2768-6_1.

Authors

Yukiteru Ono¹, Kiyoshi Asai²

Affiliations

¹ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
² Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan. asai@k.u-tokyo.ac.jp.

PMID: 36705895
DOI: 10.1007/978-1-0716-2768-6_1

Abstract

Predicting the secondary structures of RNA molecules is an essential step to characterize their functions, but the thermodynamic probability of any prediction is generally small. On the other hand, there are a few tools for calculating and visualizing various secondary structural information from RNA sequences. We implemented a web server that calculates in parallel various features of secondary structures: different types of secondary structure predictions, the marginal probabilities for local structural contexts, accessibilities of the subsequences, the energy changes by arbitrary base mutations, and the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp , which integrates software tools, CentroidFold, CentroidHomfold, IPknot, CapR, Raccess, Rchange, RintD, and RintW.

Keywords: Pseudoknot; RNA secondary structure analysis; Structure alignment; Web server.

MeSH terms

Algorithms*
Base Sequence
Internet
Nucleic Acid Conformation
RNA* / chemistry
RNA* / genetics
Sequence Analysis, RNA
Software

Substances

RNA