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Allows to analyse microRNA deep sequencing data. miRNAKey is designed to be used as a base station for the analysis of miRNA sequencing data. The main steps include: (i) searching for and removing the adaptor sequence from the 3 -ends of the reads; (ii) mapping the reads to known miRNA databases, (iii) counting reads mapped to the different miRNA species in each sample, and converting these counts into the normalized RPKM (Reads Per Kilobase Million) expression-index to allow comparison across experiments and (iv) quantifying differential expression for miRNAs between paired samples.

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miRNAKey classification

miRNAKey specifications

Software type:
Restrictions to use:
Output data:
Differential expression table (excel table), summary report, plots of post-clipping read lengths, plots of multiple-alignment rates, clipped sequence files (adaptor clipped), mapped files and sequence files, separated to mapped and non-mapped reads.
Operating system:
Unix/Linux, Mac OS
Command line interface, Graphical user interface
Input format:
Output format:
Computer skills:
Java, Burrows-Wheeler Alignment Tool, Fastx-Toolkit, the following Perl modules : Math, Spreadsheet, Getopt, GD

miRNAKey distribution


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miRNAKey support


  • Noam Shomron <>
  • miRNAKey Team <>

Additional information


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Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel; The Academic College of Tel-Aviv-Yaffo, Tel-Aviv, Israel; International Computer Science Institute, Berkeley, CA, USA; School of Computer Science and Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel

Funding source(s)

Supported by Chief Scientist Office, Ministry of Health, Israel, The Kurz-Lion Foundation, The Tel Aviv University, Faculty of Medicine, Schreiber Foundation; The Wolfson Family Charitable Fund, Israeli Science Foundation (04514831), the National Science Foundation (IIS-071325412); Faculty fellow of the Edmond Safra Bioinformatics program at Tel-Aviv University, Edmond Safra Bioinformatics Program at Tel Aviv University and the Israeli Science Foundation (04514831).

Link to literature

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