Finding RNA–Protein interaction sites using HMMs

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages8
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
ISSN (Print)10643745


  • Hidden Markov models
  • Interaction sites
  • RNA-binding proteins

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Wang, T., Yun, J., Xie, Y., & Xiao, G. (2017). Finding RNA–Protein interaction sites using HMMs. In Methods in Molecular Biology (Vol. 1552, pp. 177-184). (Methods in Molecular Biology; Vol. 1552). Humana Press Inc..