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RNA Bioinformatics

  • Book
  • © 2015

Overview

Editors:
  1. Ernesto Picardi

    1. Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research Council, University of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB), Rome, Italy

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1269)

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Table of contents (25 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. RNA Secondary and Tertiary Structures

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design

      • Alexander Churkin, Lina Weinbrand, Danny Barash
      Pages 3-16

    3. RNA Secondary Structure Prediction from Multi-Aligned Sequences

      • Michiaki Hamada
      Pages 17-38

    4. A Simple Protocol for the Inference of RNA Global Pairwise Alignments

      • Eugenio Mattei, Manuela Helmer-Citterich, Fabrizio Ferrè
      Pages 39-47

    5. De Novo Secondary Structure Motif Discovery Using RNAProfile

      • Federico Zambelli, Giulio Pavesi
      Pages 49-62

    6. Drawing and Editing the Secondary Structure(s) of RNA

      • Yann Ponty, Fabrice Leclerc
      Pages 63-100

    7. Modeling and Predicting RNA Three-Dimensional Structures

      • Jérôme Waldispühl, Vladimir Reinharz
      Pages 101-121

    8. Fast Prediction of RNA–RNA Interaction Using Heuristic Algorithm

      • Soheila Montaseri
      Pages 123-133

  3. Analysis of High-Throughput RNA Sequencing Data

    1. Front Matter

      Pages 135-135
      Download chapter PDF

    2. Quality Control of RNA-Seq Experiments

      • Xing Li, Asha Nair, Shengqin Wang, Liguo Wang
      Pages 137-146

    3. Accurate Mapping of RNA-Seq Data

      • Kin Fai Au
      Pages 147-161

    4. Quantifying Entire Transcriptomes by Aligned RNA-Seq Data

      • Raffaele A. Calogero, Francesca Zolezzi
      Pages 163-172

    5. Transcriptome Assembly and Alternative Splicing Analysis

      • Paola Bonizzoni, Gianluca Della Vedova, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi
      Pages 173-188

    6. Detection of Post-Transcriptional RNA Editing Events

      • Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Graziano Pesole
      Pages 189-205

    7. Prediction of miRNA Targets

      • Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi, Georgios A. Pavlopoulos, Panayiota Poirazi, Kriton Kalantidis et al.
      Pages 207-229

    8. Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs

      • Shahar Alon, Eli Eisenberg
      Pages 231-242

    9. NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data

      • Ilenia Boria, Lara Boatti, Igor Saggese, Flavio Mignone
      Pages 243-256

    10. e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling

      • Fosso Bruno, Marzano Marinella, Monica Santamaria
      Pages 257-278

    11. Deciphering Metatranscriptomic Data

      • Evguenia Kopylova, Laurent Noé, Corinne Da Silva, Jean-Frédéric Berthelot, Adriana Alberti, Jean-Marc Aury et al.
      Pages 279-291
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Keywords

About this book

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls.

Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

Reviews

“This text is a timely book that overviews the state of art of methodological approaches for the analysis of RNA data … . the authors often provide sufficient description of the fields and state of the art, combined with numerous references. The major advantage of the book is that it encompasses elements that attract both bioinformaticians seeking an applicability of their proposed methods and biologists seeking for answers to particular biological questions.” (Irina Ioana Mohorianu, zbMATH 1318.92003, 2015)

Editors and Affiliations

  • Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research Council, University of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB), Rome, Italy

    Ernesto Picardi

About the editor

Ernesto Picardi Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università di Bari, Bari, Italy e.picardi@biologia.uniba.it

Bibliographic Information

  • Book Title: RNA Bioinformatics

  • Editors: Ernesto Picardi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2291-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2290-1Published: 11 January 2015

  • Softcover ISBN: 978-1-4939-4644-0Published: 24 September 2016

  • eBook ISBN: 978-1-4939-2291-8Published: 10 January 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 415

  • Number of Illustrations: 29 b/w illustrations, 73 illustrations in colour

  • Topics: Bioinformatics, Protein Structure

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