RNA bioinformatics
Author(s)
Bibliographic Information
RNA bioinformatics
（Methods in molecular biology / John M. Walker, series editor, 1269）（Springer protocols）
Humana Press, 2015
- : [pbk.]
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"Softcover reprint of the hardcover 1st edition 2015"--T.p. verso
"Humana Press is a brand of Springer"--T.p. verso
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
Part I - RNA Secondary and Tertiary Structures
1. Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design
Alexander Churkin, Lina Weinbrand, and Danny Barash
2. RNA Secondary Structure Prediction from Multi-aligned Sequences
Michiaki Hamada
3. A Simple Protocol for the Inference of RNA Global Pairwise Alignments
Eugenio Mattei, Manuela Helmer Citterich, and Fabrizio Ferre
4. De Novo Secondary Structure Motif Discovery Using RNAProfile
Federico Zambelli and Giulio Pavesi
5. Drawing and Editing the Secondary Structure(s) of RNA
Yann Ponty and Fabrice Leclerc
6. Modeling and Predicting RNA Three-dimensional Structures
Jerome Waldispuhl and Vladimir Reinharz
7. Fast Prediction of RNA-RNA Interaction Using Heuristic Algorithm
Soheila Montaseri
Part II - Analysis of high-throughput RNA sequencing data
8. Quality Control of RNA-Seq Experiments
Xing Li, Asha Nair, Shengqin Wang, and Liguo Wang
9. Accurate Mapping of RNA-seq data
Kin Fai Au
10. Quantifying Entire Transcriptomes by Aligned RNA-Seq Data
Raffaele A. Calogero and Francesca Zolezzi
11. Transcriptome Assembly and Alternative Splicing Analysis
Paola Bonizzoni, Gianluca Della Vedova, Graziano Pesole, Ernesto Picardi, Yuri Pirola, and Raffaella Rizzi
12. Detection of Post-transcriptional RNA Editing Events
Ernesto Picardi, Anna Maria D'Erchia, Angela Gallo, and Graziano Pesole
13. Prediction of miRNA Targets
Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi, Georgios A. Pavlopoulos, Panayiota Poirazi, Kriton Kalantidis, and Ioannis Iliopoulos
14. Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs
Shahar Alon and Eli Eisenberg
15. NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data
Ilenia Boria, Lara Boatti, Igor Saggese, and Flavio Mignone
16. e-DNA Meta-barcoding: From NGS Raw Data to Taxonomic Profiling
Fosso Bruno, Marzano Marinella, and Monica Santamaria
17. Deciphering Metatranscriptomic Data
E. Kopylova, L. Noe, C. Da Silva, J.F. Berthelot, A. Alberti, J.M. Aury, and H. Touzet
18. RIP-Seq Data Analysis to Determine RNA-protein Associations
Federico Zambelli and Giulio Pavesi
Part III - Web resources for RNA data analysis
19. The ViennaRNA Web Services
Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz
20. Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit
Mattia D'Antonio, Ernesto Picardi, Tiziana Castrignano, Anna Maria D'Erchia, and Graziano Pesole
21. A Guideline for the Annotation of UTR Regulatory Elements in the UTRsite Collection
Matteo Giulietti, Giorgio Grillo, Sabino Liuni, and Graziano Pesole
22. Rfam: Annotating Families of Non-coding RNA Sequences
Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, and Sarah W. Burge
23. ASPicDB: A Database Web Tool for A
lternative Splicing Analysis
Mattia D'Antonio, Tiziana Castrignano, Matteo Pallocca, Anna Maria D'Erchia, Ernesto Picardi, and Graziano Pesole
24. Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista
Sylvain Foissac and Michael Sammeth
25. Computational Design of Artificial RNA Molecules For Gene Regulation
Alessandro Lagana', Dario Veneziano, Francesco Russo, Alfredo Pulvirenti, Rosalba Giugno, Carlo Maria Croce, and Alfredo Ferro
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