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Translational Research

miRDeep*

An integrated application tool for miRNA identification from RNA sequencing data

MiRDeep and its varieties are widely used to quantify known and novel miRNA from small RNA sequencing. This paper describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. MiRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and SAM/BAM format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of identified known and novel miRNAs are predicted and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation, and graphical display are purely java-coded. This application tool can be executed using a normal personal computer with only 1.5Gb of memory. Using small RNAseq data that was generated in prostate cancer (LNCaP) cells, the precision of miRNA prediction was 83.17%, 81.01% for miRDeep*, compared with 59.14%, 69.23% for miRDeep2, 80.79%, 76.6% for miRDeep, and 19.76%, 20.23% for miRanalyzer. miRDeep* also detected 35-45 novel miRNA compared with 64, 91 for miRDeep2, 39-55 for miRDeep and 848-1060 for miRanalyzer. Our benchmark of miRDeep* against miRDeep2 using a dataset where Dicer was knocked out, demonstrated that miRDeep* is less likely to result in false positive predictions of mature miRNA. Four of the novel miRNA predicted by miRDeep* were validated using stem-loop TaqMan PCR, as well as qualitative RT-PCR targeting the pre-miRNA.

miRDeep-star screen shot

Downloads

 

new version in sourceforge http://sourceforge.net/projects/mirdeepstar

manual

License

Permission to use this work is granted under the  GNU Lesser General Public License (LGPL).

Enquiries

For enquiries about the software please contact Jiyuan An (j.an@qut.edu.au) or Colleen Nelson (colleen.nelson@qut.edu.au)
Tel: +61 7 3443 7280

Related tools

miRDeep, miRDeep2, miRTRAP, MIReNA, miRDeep-P, miRanalyzer. miRNAkey, miRTools, SeqBuster, CPSS, miRGator, targetScan, picard, samtools, miRspring

Citing miRDeep*

An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737.