miARma-Seq: A Comprehensive Tool for miRNA, mRNA and circRNA Analysis

Sci Rep. 2016 May 11;6:25749. doi: 10.1038/srep25749.

Abstract

Large-scale RNAseq has substantially changed the transcriptomics field, as it enables an unprecedented amount of high resolution data to be acquired. However, the analysis of these data still poses a challenge to the research community. Many tools have been developed to overcome this problem, and to facilitate the study of miRNA expression profiles and those of their target genes. While a few of these enable both kinds of analysis to be performed, they also present certain limitations in terms of their requirements and/or the restrictions on data uploading. To avoid these restraints, we have developed a suite that offers the identification of miRNA, mRNA and circRNAs that can be applied to any sequenced organism. Additionally, it enables differential expression, miRNA-mRNA target prediction and/or functional analysis. The miARma-Seq pipeline is presented as a stand-alone tool that is both easy to install and flexible in terms of its use, and that brings together well-established software in a single bundle. Our suite can analyze a large number of samples due to its multithread design. By testing miARma-Seq in validated datasets, we demonstrate here the benefits that can be gained from this tool by making it readily accessible to the research community.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • RNA / genetics*
  • RNA / metabolism
  • RNA, Circular
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA / methods*

Substances

  • MicroRNAs
  • RNA, Circular
  • RNA, Messenger
  • RNA