Jun Ding1, Xiaoman Li2, Haiyan Hu1. 1. Department of Computer Science, University of Central Florida, Orlando, FL, USA. 2. Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA.
Abstract
MOTIVATION: The identification of microRNA (miRNA) target sites is important. In the past decade, dozens of computational methods have been developed to predict miRNA target sites. Despite their existence, rarely does a method consider the well-known competition and cooperation among miRNAs when attempts to discover target sites. To fill this gap, we developed a new approach called CCmiR, which takes the cooperation and competition of multiple miRNAs into account in a statistical model to predict their target sites. RESULTS: Tested on four different datasets, CCmiR predicted miRNA target sites with a high recall and a reasonable precision, and identified known and new cooperative and competitive miRNAs supported by literature. Compared with three state-of-the-art computational methods, CCmiR had a higher recall and a higher precision. AVAILABILITY AND IMPLEMENTATION: CCmiR is freely available at http://hulab.ucf.edu/research/projects/miRNA/CCmiR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The identification of microRNA (miRNA) target sites is important. In the past decade, dozens of computational methods have been developed to predict miRNA target sites. Despite their existence, rarely does a method consider the well-known competition and cooperation among miRNAs when attempts to discover target sites. To fill this gap, we developed a new approach called CCmiR, which takes the cooperation and competition of multiple miRNAs into account in a statistical model to predict their target sites. RESULTS: Tested on four different datasets, CCmiR predicted miRNA target sites with a high recall and a reasonable precision, and identified known and new cooperative and competitive miRNAs supported by literature. Compared with three state-of-the-art computational methods, CCmiR had a higher recall and a higher precision. AVAILABILITY AND IMPLEMENTATION: CCmiR is freely available at http://hulab.ucf.edu/research/projects/miRNA/CCmiR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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