PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

Genome Biol. 2011 Aug 18;12(8):R79. doi: 10.1186/gb-2011-12-8-r79.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism
  • Binding Sites / genetics*
  • Databases, Genetic
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Immunoprecipitation / instrumentation
  • Immunoprecipitation / methods*
  • Linear Models
  • MicroRNAs / genetics
  • MicroRNAs / metabolism
  • RNA / isolation & purification*
  • RNA / metabolism
  • Sequence Analysis, RNA / methods*
  • Signal-To-Noise Ratio
  • Transcriptome


  • Argonaute Proteins
  • MicroRNAs
  • RNA