title: Finding RNA-Protein Interaction Sites Using HMMs.
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.
authors.affiliation: Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.affiliation: Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA.
authors.forename: Jonghyun
authors.initials: J
authors.lastname: Yun
authors.affiliation: Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA. Guanghua.Xiao@UTSouthwestern.edu.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Xiao
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation; D008390:Markov Chains; D012313:RNA / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: Hidden Markov models; Interaction sites; RNA-binding proteins