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

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

Author information

1
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.

Abstract

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/.

PMID:
21851591
PMCID:
PMC3302668
DOI:
10.1186/gb-2011-12-8-r79
[Indexed for MEDLINE]
Free PMC Article

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