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Web Services for RNA-RNA Interaction Prediction

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RNA Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2586))

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Abstract

Non-coding RNAs have various biological functions such as translational regulation, and RNA-RNA interactions play essential roles in the mechanisms of action of these RNAs. Therefore, RNA-RNA interaction prediction is an important problem in bioinformatics, and many tools have been developed for the computational prediction of RNA-RNA interactions. In addition to the development of novel algorithms with high accuracy, the development and maintenance of web services is essential for enhancing usability by experimental biologists. In this review, we survey web services for RNA-RNA interaction predictions and introduce how to use primary web services. We present various prediction tools, including general interaction prediction tools, prediction tools for specific RNA classes, and RNA-RNA interaction-based RNA design tools. Additionally, we discuss the future perspectives of the development of RNA-RNA interaction prediction tools and the sustainability of web services.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan

    Tsukasa Fukunaga

  2. Waseda Institute for Advanced Study, Waseda University, Tokyo, Japan

    Tsukasa Fukunaga

  3. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    Junichi Iwakiri

  4. Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan

    Michiaki Hamada

  5. Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

    Michiaki Hamada

Authors
  1. Tsukasa Fukunaga
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  2. Junichi Iwakiri
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  3. Michiaki Hamada
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Correspondence to Tsukasa Fukunaga .

Editor information

Editors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Risa Karakida Kawaguchi

  2. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    Junichi Iwakiri

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Fukunaga, T., Iwakiri, J., Hamada, M. (2023). Web Services for RNA-RNA Interaction Prediction. In: Kawaguchi, R.K., Iwakiri, J. (eds) RNA Structure Prediction. Methods in Molecular Biology, vol 2586. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2768-6_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2768-6_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2767-9

  • Online ISBN: 978-1-0716-2768-6

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