PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
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/.
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Related Subject Headings
- Transcriptome
- Signal-To-Noise Ratio
- Sequence Analysis, RNA
- RNA
- MicroRNAs
- Linear Models
- Immunoprecipitation
- Humans
- High-Throughput Nucleotide Sequencing
- Databases, Genetic
Citation
Published In
DOI
EISSN
Publication Date
Volume
Issue
Start / End Page
Location
Related Subject Headings
- Transcriptome
- Signal-To-Noise Ratio
- Sequence Analysis, RNA
- RNA
- MicroRNAs
- Linear Models
- Immunoprecipitation
- Humans
- High-Throughput Nucleotide Sequencing
- Databases, Genetic