miRNAgFree is a novel microRNA prediction approach based on biogenesis features, such as the known 5' fluctuation, and duplex mean free energies which does not require a genome assembly. We found that, in general, biogenesis related parameters are far more discriminative than duplex related structural parameters.
- OpenJDK 1.8.0 or higher (64-bit) or JRE 8 or higher (64-bit).
- RNAcofold from Vienna Package 2.0 or higher (64-bit).
- Bowtie (optional) 1.2.2 or higher (64-bit).
- SRA Toolkit (optional) 2.8.0 or higher (64-bit).
sudo apt-get install unzip default-jre
sudo apt-add-repository ppa:j-4/vienna-rna
sudo apt-get update
sudo apt-get install vienna-rna
wget -c http://bioinfo2.ugr.es:8080/ceUGR/wp-content/uploads/2017/08/miRNAgFree.zip
unzip miRNAgFree.zip
java –jar miRNAgFree.jar input=example_input.fa output=example_output_folder RNAcofold=./RNAcofold
java –jar miRNAgFree.jar input=example_input.fa output=example_output_folder
This software was developped and is mantained by Michael Hackenber at University of Granada. Please contact him via hackenberg@go.ugr.es.
© 2018 Computational Epigenomics Lab, Evolutionary Genomics and Bioinformatics Group. Dept. of Genetics, Inst. of Biotechnology, University of Granada, Spain