Introduction

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/.

Publications

  1. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
    Cite this
    Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U, 2011-08-01 - Genome biology

Credits

  1. David L Corcoran
    Developer

    Institute for Genome Sciences and Policy, Duke University, United States of America

  2. Stoyan Georgiev
    Developer

  3. Neelanjan Mukherjee
    Developer

  4. Eva Gottwein
    Developer

  5. Rebecca L Skalsky
    Developer

  6. Jack D Keene
    Developer

  7. Uwe Ohler
    Investigator

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Summary
AccessionBT000489
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByUwe Ohler