Finding RNA–Protein interaction sites using HMMs

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages177-184
Number of pages8
Volume1552
DOIs
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1552
ISSN (Print)10643745

Fingerprint

RNA-Binding Proteins
RNA
Computational Biology
Immunoprecipitation
Cell Culture Techniques
Binding Sites
Genome
Datasets

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

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.. https://doi.org/10.1007/978-1-4939-6753-7_13

Finding RNA–Protein interaction sites using HMMs. / Wang, Tao; Yun, Jonghyun; Xie, Yang; Xiao, Guanghua.

Methods in Molecular Biology. Vol. 1552 Humana Press Inc., 2017. p. 177-184 (Methods in Molecular Biology; Vol. 1552).

Research output: Chapter in Book/Report/Conference proceedingChapter

Wang, T, Yun, J, Xie, Y & Xiao, G 2017, Finding RNA–Protein interaction sites using HMMs. in Methods in Molecular Biology. vol. 1552, Methods in Molecular Biology, vol. 1552, Humana Press Inc., pp. 177-184. https://doi.org/10.1007/978-1-4939-6753-7_13
Wang T, Yun J, Xie Y, Xiao G. Finding RNA–Protein interaction sites using HMMs. In Methods in Molecular Biology. Vol. 1552. Humana Press Inc. 2017. p. 177-184. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-6753-7_13
Wang, Tao ; Yun, Jonghyun ; Xie, Yang ; Xiao, Guanghua. / Finding RNA–Protein interaction sites using HMMs. Methods in Molecular Biology. Vol. 1552 Humana Press Inc., 2017. pp. 177-184 (Methods in Molecular Biology).
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