RNA bioinformatics / edited by Ernesto Picardi.

Contributor(s): Picardi, Ernesto [editor.]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1269.Publisher: New York, NY : Humana Press : Springer, [2015]Copyright date: ©2015Description: 1 online resource (xii, 415 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781493922918; 1493922912; 1493922904; 9781493922901Subject(s): Bioinformatics | Computational biology | RNA -- Biotechnology | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Biological Science Disciplines | Biology | Chemicals and Drugs | Computational Biology | Disciplines and Occupations | Genetic Techniques | Investigative Techniques | Natural Science Disciplines | Nucleic Acids, Nucleotides, and Nucleosides | Nucleic Acids | RNA | Sequence Analysis, RNA | Sequence Analysis | Molecular biology | Proteins | Science -- Life Sciences -- Anatomy & Physiology | Science -- Life Sciences -- Biochemistry | Bioinformatics | Computational biology | RNA -- BiotechnologyGenre/Form: Laboratory Manual. | Electronic books. Additional physical formats: Print version:: RNA bioinformatics.DDC classification: 572.80285 LOC classification: QH324.2Online resources: Click here to access online
Contents:
Free energy minimization to predict RNA secondary structures and computational RNA design / Alexander Churkin, Lina Weinbrand, and Danny Barash -- RNA secondary structure prediction from multi-aligned sequences / Michiaki Hamada -- Simple protocol for the inference of RNA global pairwise alignments / Eugenio Mattei, Manuela Helmer-Citterich, and Fabrizio Ferrè -- De novo secondary structure motif discovery using RNA profile / Federico Zambelli and Giulio Pavesi -- Drawing and editing the secondary structure(s) of RNA / Yann Ponty and Fabrice Leclerc -- Modeling and predicting RNA three-dimensional structures / Jérôme Waldispühl and Vladimir Reinharz -- Fast prediction of RNA-RNA interaction using heuristic algorithm / Soheila Montaseri -- Quality control of RNA-Seq experiments / Xing Li ... [and 3 others] -- Accurate mapping of RNA-Seq data / Kin Fai Au -- Quantifying entire transcriptomes by aligned RNA-Seq data / Raffaele A. Calogero and Francesca Zolezzi -- Transcriptome assembly and alternative splicing analysis / Paola Bonizzoni ... [and 5 others] -- Detection of post-transcriptional RNA editing events / Ernesto Picardi ... [and 3 others] -- Prediction of miRNA targets / Anastasis Oulas ... [and 6 others] -- Using deep sequencing data for identification of editing sites in mature miRNAs / Shahar Alon and Eli Eisenberg -- NGS-trex : an automatic analysis workflow for RNA-seq data / Ilenia Boria ... [and 3 others] -- e-DNA meta-barcoding : from NGS raw data to taxonomic profiling / Fosso Bruno, Marzano Marinella, and Monica Santamaria -- Deciphering metatranscriptomic data / Evguenia Kopylova ... [and 6 others] -- RIP-seq data analysis to determine RNA-protein associations / Federico Zambelli and Giulio Pavesi -- ViennaRNA eeb services / Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz -- Exploring the RNA editing potential of RNA-Seq data by ExpEdit / Mattia D'Antonio ... [and 4 others] -- Guideline for the annotation of UTR regulatory elements in the UTRsite collection / Matteo Giulietti ... [and 3 others] -- Rfam : annotating families of non-coding RNA sequences / Jennifer Daub ... [and 3 others] -- ASPicDB : a database web tool for alternative splicing analysis / Mattia D'Antonio ... [and 5 others] -- Analysis of alternative splicing events in custom gene datasets by AStalavista / Sylvain Foissac and Michael Sammeth -- Computational design of artificial RNA molecules for gene regulation / Alessandro Laganà ... [and 6 others].
Summary: 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."
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Includes bibliographical references and index.

Free energy minimization to predict RNA secondary structures and computational RNA design / Alexander Churkin, Lina Weinbrand, and Danny Barash -- RNA secondary structure prediction from multi-aligned sequences / Michiaki Hamada -- Simple protocol for the inference of RNA global pairwise alignments / Eugenio Mattei, Manuela Helmer-Citterich, and Fabrizio Ferrè -- De novo secondary structure motif discovery using RNA profile / Federico Zambelli and Giulio Pavesi -- Drawing and editing the secondary structure(s) of RNA / Yann Ponty and Fabrice Leclerc -- Modeling and predicting RNA three-dimensional structures / Jérôme Waldispühl and Vladimir Reinharz -- Fast prediction of RNA-RNA interaction using heuristic algorithm / Soheila Montaseri -- Quality control of RNA-Seq experiments / Xing Li ... [and 3 others] -- Accurate mapping of RNA-Seq data / Kin Fai Au -- Quantifying entire transcriptomes by aligned RNA-Seq data / Raffaele A. Calogero and Francesca Zolezzi -- Transcriptome assembly and alternative splicing analysis / Paola Bonizzoni ... [and 5 others] -- Detection of post-transcriptional RNA editing events / Ernesto Picardi ... [and 3 others] -- Prediction of miRNA targets / Anastasis Oulas ... [and 6 others] -- Using deep sequencing data for identification of editing sites in mature miRNAs / Shahar Alon and Eli Eisenberg -- NGS-trex : an automatic analysis workflow for RNA-seq data / Ilenia Boria ... [and 3 others] -- e-DNA meta-barcoding : from NGS raw data to taxonomic profiling / Fosso Bruno, Marzano Marinella, and Monica Santamaria -- Deciphering metatranscriptomic data / Evguenia Kopylova ... [and 6 others] -- RIP-seq data analysis to determine RNA-protein associations / Federico Zambelli and Giulio Pavesi -- ViennaRNA eeb services / Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz -- Exploring the RNA editing potential of RNA-Seq data by ExpEdit / Mattia D'Antonio ... [and 4 others] -- Guideline for the annotation of UTR regulatory elements in the UTRsite collection / Matteo Giulietti ... [and 3 others] -- Rfam : annotating families of non-coding RNA sequences / Jennifer Daub ... [and 3 others] -- ASPicDB : a database web tool for alternative splicing analysis / Mattia D'Antonio ... [and 5 others] -- Analysis of alternative splicing events in custom gene datasets by AStalavista / Sylvain Foissac and Michael Sammeth -- Computational design of artificial RNA molecules for gene regulation / Alessandro Laganà ... [and 6 others].

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."

Online resource; title from PDF title page (SpringerLink, viewed January 23, 2015).

English.

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