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Erhard, Florian; Doelken, Lars; Jaskiewicz, Lukasz; Zimmer, Ralf (2013): PARma: identification of microRNA target sites in AGO-PAR-CLIP data. In: Genome Biology 14:R79


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