PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Genome Biol
; 12(8): R79, 2011 Aug 18.
Article
en En
| MEDLINE
| ID: mdl-21851591
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/.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Sitios de Unión
/
ARN
/
Análisis de Secuencia de ARN
/
Inmunoprecipitación
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Año:
2011
Tipo del documento:
Article