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PARma: identification of microRNA target sites in AGO-PAR-CLIP data

Florian Erhard1*, Lars Dölken2, Lukasz Jaskiewicz3 and Ralf Zimmer1

Author affiliations

1 Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany

2 Department of Medicine, University of Cambridge, Box 157, Level 5, Addenbrooke's Hospital, Hills Road, CB2 0QQ Cambridge, UK

3 Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstr. 50/70, CH-4056, Basel, Switzerland

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Citation and License

Genome Biology 2013, 14:R79  doi:10.1186/gb-2013-14-7-r79

Published: 29 July 2013


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 webcite

PAR-CLIP; microRNA; generative model; EM algorithm