Rtools: a web server for various secondary structural analyses on single RNA sequences

Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as 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 and RintD.

Original languageEnglish
Pages (from-to)W302-W307
JournalNucleic acids research
Volume44
Issue numberW1
DOIs
Publication statusPublished - 2016 Jul 8
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Hamada, M., Ono, Y., Kiryu, H., Sato, K., Kato, Y., Fukunaga, T., Mori, R., & Asai, K. (2016). Rtools: a web server for various secondary structural analyses on single RNA sequences. Nucleic acids research, 44(W1), W302-W307. https://doi.org/10.1093/nar/gkw337