PARma: identification of microRNA target sites in AGO-PAR-CLIP data.
Genome Biol, 2013/7/29;14(7):R79.
Erhard F, Dölken L, Jaskiewicz L, Zimmer R
PMID: 23895117DOI: 10.1186/gb-2013-14-7-r79
Impact factor: 17.906
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.
MeSH terms
Algorithms; Argonaute Proteins; B-Lymphocytes; Cluster Analysis; Humans; Immunoprecipitation; MicroRNAs; Models, Genetic; Reproducibility of Results; Ribonucleosides; Software
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