title: miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis.
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.
authors.affiliation: Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Computational Biology and Bioinformatics Group, Seville, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Andrés-León
authors.affiliation: Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Computational Biology and Bioinformatics Group, Seville, Spain.
authors.forename: Rocío
authors.initials: R
authors.lastname: Núñez-Torres
authors.affiliation: Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Computational Biology and Bioinformatics Group, Seville, Spain.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Rojas
mesh_terms: D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D000079962:RNA, Circular; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D000079962:RNA, Circular; D012333:RNA, Messenger; D012313:RNA