miARma-Seq – a comprehensive tool for miRNA, mRNA and circRNA analysis

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, researchers from the CSIC/University of Seville 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. This suite can analyze a large number of samples due to its multithread design. By testing miARma-Seq in validated datasets, the researchers demonstrate here the benefits that can be gained from this tool by making it readily accessible to the research community.

An overview of the modular design of the pipeline. Main modules are indicated by gray background. Output files are indicated by purple background.

Availability – The miARma-Seq tools are avialable at: http://miarmaseq.cbbio.es/

Andrés-León E, Núñez-Torres R, Rojas AM. (2016) miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Sci Rep 6:25749. [article]

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