Chapter title |
RIP-Seq Data Analysis to Determine RNA–Protein Associations
|
---|---|
Chapter number | 18 |
Book title |
RNA Bioinformatics
|
Published in |
Methods in molecular biology, December 2014
|
DOI | 10.1007/978-1-4939-2291-8_18 |
Pubmed ID | |
Book ISBNs |
978-1-4939-2290-1, 978-1-4939-2291-8
|
Authors |
Federico Zambelli, Giulio Pavesi |
Editors |
Ernesto Picardi |
Abstract |
Next-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the identification of the RNAs bound by a given RBP. |
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