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Finding RNA–Protein Interaction Sites Using HMMs

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1552)

Abstract

RNA-binding proteins play important roles in the various stages of RNA maturation through binding to its target RNAs. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Several Hidden Markov model-based (HMM) approaches have been suggested to identify protein–RNA binding sites from CLIP-Seq datasets. In this chapter, we describe how HMM can be applied to analyze CLIP-Seq datasets, including the bioinformatics preprocessing steps to extract count information from the sequencing data before HMM and the downstream analysis steps following peak-calling.

Key words

Hidden Markov models RNA-binding proteins Interaction sites 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of MathematicsUniversity of Texas at ArlingtonArlingtonUSA
  2. 2.Quantitative Biomedical Research Center, Department of Clinical ScienceUniversity of Texas Southwestern Medical CenterDallasUSA

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