RNA Bioinformatics

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.

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 Ferrè

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
Jérôme Waldispühl 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. Noé, 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 Castrignanò, 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

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