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

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


  • eng

Conference Location

  • England