MIRPIPE

MIRPIPE is a browser-based application for the identification and quantification of microRNAs (miRNAs) using homology detection. The tool automatically trims raw RNA-Seq reads from various sequencing instruments, processes isomiRs, and quantifies detected miRNAs against public or user-uploaded reference databases. MIRPIPE is freely available as a web service and was implemented in Perl, integrated into Galaxy, and an offline version for local execution is also available. The tool is useful for analyzing miRNAs in niche model organisms lacking genomic sequences.

Topic

RNA;Functional, regulatory and non-coding RNA

Detail

  • Operation: Prediction and recognition

  • Software interface: Web user interface

  • Language: Perl

  • License: Other

  • Cost: Free

  • Version name: 1.2

  • Credit: Excellence Cluster Cardio-Pulmonary System (ECCPS).

  • Input: -

  • Output: -

  • Contact: Carsten Künne carsten.kuenne@mpi-bn.mpg.de, Jens Preußner jens.preussner@mpi-bn.mpg.de, Mario Looso mario.looso@mpi-bn.mpg.de

  • Collection: -

  • Maturity: -

Publications

  • MIRPIPE: quantification of microRNAs in niche model organisms.
  • Kuenne C, et al. MIRPIPE: quantification of microRNAs in niche model organisms. MIRPIPE: quantification of microRNAs in niche model organisms. 2014; 30:3412-3. doi: 10.1093/bioinformatics/btu573
  • https://doi.org/10.1093/bioinformatics/btu573
  • PMID: 25165094
  • PMC: PMC4816158

Download and documentation

    Currently not available or not maintained.

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