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

Item Type:Article
Title:PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
Creators Name:Corcoran, D.L. and Georgiev, S. and Mukherjee, N. and Gottwein, E. and Skalsky, R.L. and Keene, J.D. and Ohler, U.
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/.
Keywords:Argonaute Proteins, Binding Sites, Genetic Databases, High-Throughput Nucleotide Sequencing, Immunoprecipitation, Linear Models, MicroRNAs, RNA, RNA Sequence Analysis, Signal-To-Noise Ratio, Transcriptome
Source:Genome Biology
Publisher:BioMed Central
Page Range:R79
Date:18 August 2011
Official Publication:https://doi.org/10.1186/gb-2011-12-8-r79
PubMed:View item in PubMed

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