title: PARma: identification of microRNA target sites in AGO-PAR-CLIP data.
abstract: PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma.
authors.forename: Florian
authors.initials: F
authors.lastname: Erhard
authors.forename: Lars
authors.initials: L
authors.lastname: Dölken
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaskiewicz
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
mesh_terms: D000465:Algorithms; D060565:Argonaute Proteins / Q000378:metabolism*; D001402:B-Lymphocytes; D016000:Cluster Analysis; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000235:genetics*; D008957:Models, Genetic; D015203:Reproducibility of Results; D012263:Ribonucleosides / Q000378:metabolism*; D012984:Software
chemical_list: D060565:Argonaute Proteins; D035683:MicroRNAs; D012263:Ribonucleosides
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