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.

SUBMITTER: Erhard F 

PROVIDER: S-EPMC4054675 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature