RNA Structure Prediction

1. Front Matter

   Pages i-xxii

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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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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.

• RNA secondary structure
• In silico structure prediction
• 3D structure analyses
• Machine learning
• RNA 3D structure databases
• Computational prediction and design

• 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

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