RIP-Seq data analysis to determine RNA-protein associations

Methods Mol Biol. 2015:1269:293-303. doi: 10.1007/978-1-4939-2291-8_18.


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.

MeSH terms

  • Computational Biology
  • High-Throughput Nucleotide Sequencing / methods*
  • Protein Binding
  • RNA / genetics
  • RNA / metabolism*


  • RNA