RNA Bioinformatics – New RNA-Seq Protocols from Methods in Molecular Biology

RNA Bioinformatics

Edited by Ernesto Picardi ISBN: 978-1-4939-2290-1 (Print) 978-1-4939-2291-8 (Online)

Analysis of High-Throughput RNA Sequencing Data

Quality Control of RNA-Seq Experiments
Xing Li, Asha Nair, Shengqin Wang, Liguo Wang
Pages 137-146

Accurate Mapping of RNA-Seq Data
Kin Fai Au
Pages 147-161

Quantifying Entire Transcriptomes by Aligned RNA-Seq Data
Raffaele A. Calogero, Francesca Zolezzi
Pages 163-172

Transcriptome Assembly and Alternative Splicing Analysis
Paola Bonizzoni, Gianluca Della Vedova, Graziano Pesole, Ernesto Picardi, Yuri Pirola
Pages 173-188

Detection of Post-Transcriptional RNA Editing Events
Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Graziano Pesole
Pages 189-205

Prediction of miRNA Targets
Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi, Georgios A. Pavlopoulos
Pages 207-229

Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs
Shahar Alon, Eli Eisenberg
Pages 231-242

NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data
Ilenia Boria, Lara Boatti, Igor Saggese, Flavio Mignone
Pages 243-256

e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling
Fosso Bruno, Marzano Marinella, Monica Santamaria
Pages 257-278

Deciphering Metatranscriptomic Data
Evguenia Kopylova, Laurent Noé, Corinne Da Silva, Jean-Frédéric Berthelot
Pages 279-291

RIP-Seq Data Analysis to Determine RNA–Protein Associations
Federico Zambelli, Giulio Pavesi
Pages 293-303

Web Resources for RNA Data Analysis

The ViennaRNA Web Services
Andreas R. Gruber, Stephan H. Bernhart, Ronny Lorenz
Pages 307-326

Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit
Mattia D’Antonio, Ernesto Picardi, Tiziana Castrignanò, Anna Maria D’Erchia
Pages 327-338

A Guideline for the Annotation of UTR Regulatory Elements in the UTRsite Collection
Matteo Giulietti, Giorgio Grillo, Sabino Liuni, Graziano Pesole
Pages 339-348

Rfam: Annotating Families of Non-Coding RNA Sequences
Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Sarah W. Burge
Pages 349-363

ASPicDB: A Database Web Tool for Alternative Splicing Analysis
Mattia D’Antonio, Tiziana Castrgnanò, Matteo Pallocca, Anna Maria D’Erchia
Pages 365-378

Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista
Sylvain Foissac, Michael Sammeth
Pages 379-392

Computational Design of Artificial RNA Molecules for Gene Regulation
Alessandro Laganà, Dario Veneziano, Francesco Russo, Alfredo Pulvirenti, Rosalba Giugno
Pages 393-412

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