miRMaster – web-based NGS data analysis of human microRNAs

The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data Saarland University researchers implemented the fast, accurate and comprehensive web-based tool miRMaster. Their toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, their analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, the researchers designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction.

Schematic workflow of miRMaster

rna-seq

The bar at the left shows the runtime impact of each step. Steps performed by the user are shown in orange and steps performed by the server in blue.

MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, these predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them.

Availability – MiRMaster is available at: http://www.ccb.uni-saarland.de/mirmaster

Fehlmann T, Backes C, Kahraman M, Haas J, Ludwig N, Posch AE, Würstle ML, Hübenthal M, Franke A, Meder B, Meese E, Keller A. (2017) Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. Nucleic Acids Res 45(15):8731-8744. [article]

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