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RNA Structure Prediction

  • Book
  • © 2023

Overview

Editors:
  1. Risa Karakida Kawaguchi

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

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    You can also search for this editor in PubMed   Google Scholar

  2. Junichi Iwakiri

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

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

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xxii
    Download chapter PDF

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

    • Yukiteru Ono, Kiyoshi Asai
    Pages 1-14

  3. Linear-Time Algorithms for RNA Structure Prediction

    • He Zhang, Liang Zhang, Kaibo Liu, Sizhen Li, David H. Mathews, Liang Huang
    Pages 15-34

  4. Genome-Wide RNA Secondary Structure Prediction

    • Risa Karakida Kawaguchi, Hisanori Kiryu
    Pages 35-48

  5. Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User’s Guide to the LandscapeFold Algorithm

    • Ofer Kimchi, Michael P. Brenner, Lucy J. Colwell
    Pages 49-77

  6. Metrics for RNA Secondary Structure Comparison

    • Feiqi Wang, Tatsuya Akutsu, Tomoya Mori
    Pages 79-88

  7. RNA Secondary Structure Prediction Based on Energy Models

    • Manato Akiyama, Kengo Sato
    Pages 89-105

  8. RNA Secondary Structure Alteration Caused by Single Nucleotide Variants

    • Risa Karakida Kawaguchi, Hisanori Kiryu
    Pages 107-120

  9. Evolutionary Conservation of RNA Secondary Structure

    • Maria Beatriz Walter Costa
    Pages 121-146

  10. Network-Based Structural Alignment of RNA Sequences Using TOPAS

    • Chun-Chi Chen, Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
    Pages 147-162

  11. Fast RNA-RNA Interaction Prediction Methods for Interaction Analysis of Transcriptome-Scale Large Datasets

    • Tsukasa Fukunaga, Michiaki Hamada
    Pages 163-173

  12. Web Services for RNA-RNA Interaction Prediction

    • Tsukasa Fukunaga, Junichi Iwakiri, Michiaki Hamada
    Pages 175-195

  13. ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks

    • Peter K. Koo, Matt Ploenzke, Praveen Anand, Steffan Paul, Antonio Majdandzic
    Pages 197-215

  14. RNA Structure Determination by High-Throughput Structural Analysis

    • Naoki Takizawa
    Pages 217-231

  15. RNA 3D Modeling with FARFAR2, Online

    • Andrew M. Watkins, Rhiju Das
    Pages 233-249

  16. Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake

    • Chris P. Jurich, Joseph D. Yesselman
    Pages 251-261

  17. RNA 3D Structure Comparison Using RNA-Puzzles Toolkit

    • Marcin Magnus, Zhichao Miao
    Pages 263-285

  18. Correction to: RNA Structure Prediction

    • Risa Karakida Kawaguchi, Junichi Iwakiri
    Pages C1-C1

  19. Back Matter

    Pages 287-290
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Keywords

About this book

This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. 

Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.

Editors and Affiliations

  • Cold Spring Harbor Laboratory, Cold Spring Harbor, USA

    Risa Karakida Kawaguchi

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

    Junichi Iwakiri

Bibliographic Information

  • Book Title: RNA Structure Prediction

  • Editors: Risa Karakida Kawaguchi, Junichi Iwakiri

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2767-9Published: 28 January 2023

  • Softcover ISBN: 978-1-0716-2770-9Published: 28 January 2024

  • eBook ISBN: 978-1-0716-2768-6Published: 27 January 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XXII, 290

  • Number of Illustrations: 17 b/w illustrations, 89 illustrations in colour

  • Topics: Theoretical and Computational Chemistry, Genetics and Genomics

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