PROmiRNA is a program for annotating miRNA promoters in human, as well as other species. It uses deepCAGE data from the FANTOM4 Consortium and integrated cage tag counts and other promoter features, such as CpG content, conservation and TATA box affinity, to score the potential of a candidate regions to be a promoter. Given a list of genomic regions of interest, in the form of a gff file, PROmiRNA returns the most probable promoter locations, together with the posterior probabilities calculated by the model. More informations on how to run PROmiRNA on your regions of interest can be found in the README file inside the PROmiRNA directory. The source code of PROmiRNA, as well as the external data necessary to run the program, can be downloaded at the links below.
PROmiRNA is based on the miRBase annotation. If you are using an old miRBase version (equal or lower than 18) please use a old version of PROmiRNA, available at the following link
From the following link you can download the repeat file for mm9 (derived from UCSC)
From the following link you can download the repeat file for mm10 (derived from UCSC)