miRNA prediction

miRDeep2 is a software package which can be used for identification of novel and known miRNAs in deep sequencing data and for miRNA expression profiling across samples.

Here miRDeep2 is coupled with the SeqTrimMap algorithm that maps reads using a sequential trimming strategy which allows an efficient mapping of short reads.


This tool uses miRDeep2 and SeqTrimMap, which are licensed separately.


miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
M.R. Friedländer, S.D. Mackowiak, N. Li, W. Chen, N. Rajewsky.
Nucleic Acids Research (2012) 40 (1): 37-52.
Detection of microRNAs in color space.
A. Marco and S. Griffiths-Jones.
Bioinformatics (2012) 28 (3): 318-323.