RNA Structure Prediction

ISBN-13: 9781071627679 / Angielski / Twarda / 2023 / 290 str.

Risa Karakida Kawaguchi; Junichi Iwakiri

Opis

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.

Spis treści

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

            Yukiteru Ono and Kiyoshi Asai

 

2. Linear-Time Algorithms for RNA Structure Prediction

            He Zhang, Liang Zhang, Kaibo Liu, Sizhen Li, David H. Mathews, and Liang Huang

 

3. Genome-Wide RNA Secondary Structure Prediction

            Risa Karakida Kawaguchi and Hisanori Kiryu

 

4. Nucleic Acid Structure Prediction Including Pseudoknots through Direct Enumeration of States: A User's Guide to the LandscapeFold Algorithm

            Ofer Kimchi, Michael P. Brenner, and Lucy J. Colwell

 

5. Metrics for RNA Secondary Structure Comparison

            Feiqi Wang, Tatsuya Akutsu, and Tomoya Mori

 

6. RNA Secondary Structure Prediction Based on Energy Models

            Manato Akiyama and Kengo Sato

 

7. RNA Secondary Structure Alteration Caused by Single Nucleotide Variants

            Risa Karakida Kawaguchi and Hisanori Kiryu

 

8. Evolutionary Conservation of RNA Secondary Structure

            Maria Beatriz Walter Costa

 

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

            Chun-Chi Chen, Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon

 

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

            Tsukasa Fukunaga and Michiaki Hamada

 

11. Web Services for RNA-RNA Interaction Prediction

            Tsukasa Fukunaga, Junichi Iwakiri, and Michiaki Hamada

 

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

            Peter K. Koo, Matt Ploenzke, Praveen Anand, Steffan Paul, and Antonio Majdandzic

 

13. RNA Structure Determination by High-Throughput Structural Analysis

            Naoki Takizawa

 

14. RNA 3D Modeling with FARFAR2, Online

            Andrew Watkins and Rhiju Das

 

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

            Chris P. Jurich and Joseph D. Yesselman

 

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

            Marcin Magnus and Zhichao Miao