Introduction

Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).

Publications

  1. mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs.
    Cite this
    Shi J, Dong M, Li L, Liu L, Luz-Madrigal A, Tsonis PA, Del Rio-Tsonis K, Liang C, 2015-10-01 - Scientific reports

Credits

  1. Jieming Shi
    Developer

    Department of Biology, Miami University and Center for Visual Sciences at Miami University, United States of America

  2. Min Dong
    Developer

    Department of Biology, Miami University and Center for Visual Sciences at Miami University, United States of America

  3. Lei Li
    Developer

    Department of Biology, Miami University and Center for Visual Sciences at Miami University, United States of America

  4. Lin Liu
    Developer

    Department of Biology, Miami University and Center for Visual Sciences at Miami University, United States of America

  5. Agustin Luz-Madrigal
    Developer

    Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), United States of America

  6. Panagiotis A Tsonis
    Developer

    Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), United States of America

  7. Katia Del Rio-Tsonis
    Developer

    Department of Biology, Miami University and Center for Visual Sciences at Miami University, United States of America

  8. Chun Liang
    Investigator

    Department of Computer Science and Software Engineering, Miami University, United States of America

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Summary
AccessionBT000947
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByChun Liang