PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Journal Article (Journal Article)
Crosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking. We present an approach, centered on the novel PARalyzer tool, for mapping high-confidence sites from PAR-CLIP deep-sequencing data. We show that PARalyzer delineates sites with a high signal-to-noise ratio. Motif finding identifies the sequence preferences of RNA-binding proteins, as well as seed-matches for highly expressed microRNAs when profiling Argonaute proteins. Our study describes tailored analytical methods and provides guidelines for future efforts to utilize high-throughput sequencing in RNA biology. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer/.
Full Text
Duke Authors
Cited Authors
- Corcoran, DL; Georgiev, S; Mukherjee, N; Gottwein, E; Skalsky, RL; Keene, JD; Ohler, U
Published Date
- August 18, 2011
Published In
Volume / Issue
- 12 / 8
Start / End Page
- R79 -
PubMed ID
- 21851591
Pubmed Central ID
- PMC3302668
Electronic International Standard Serial Number (EISSN)
- 1474-760X
Digital Object Identifier (DOI)
- 10.1186/gb-2011-12-8-r79
Language
- eng
Conference Location
- England