Introduction

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases.The Web service is freely available at http://bioinformatics.mpi-bn.mpg.de. MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our Web site.

Publications

  1. MIRPIPE: quantification of microRNAs in niche model organisms.
    Cite this
    Kuenne C, Preussner J, Herzog M, Braun T, Looso M, 2014-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Carsten Kuenne
    Developer

    Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Germany

  2. Jens Preussner
    Developer

    Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Germany

  3. Mario Herzog
    Developer

    Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Germany

  4. Thomas Braun
    Developer

    Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Germany

  5. Mario Looso
    Investigator

    Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Germany

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Summary
AccessionBT001862
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByMario Looso