Finding RNA–Protein Interaction Sites Using HMMs
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 wordsHidden Markov models RNA-binding proteins Interaction sites
- 8.Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J et al (2010) PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 41. doi: 10.3791/2034. pii: 2034
- 17.Welch LR (2003) Hidden Markov models and the Baum-Welch algorithm. IEEE Inform Theory Soc Newslett:1–14Google Scholar