MiRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase

Taosheng Xu,Jie Gui,Thuc Duy Le,Kui Yu,Junpeng Zhang,Hongqiang Wang,Ning Su,Lin Liu,Weijia Zhang,Jiuyong Li

doi:10.1186/s12859-018-2531-5

Abstract

BackgroundmiRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses.ResultsWe introduce miRBaseConverter, an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/miRBaseConverter/). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application at http://nugget.unisa.edu.au:3838/miRBaseConverter. miRBaseConverter has a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources.ConclusionsThe Bioconductor package miRBaseConverter and the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.

Highlights

MicroRNAs are short non-coding RNA molecules that are widely encoded by eukaryotic nuclear DNA in plants and animals, and by viral DNA in some viruses [1, 2]. miRNAs are one of the vital and evolutionarily molecules that play an important role in post-transcriptional regulation by promoting degradation and repressing translation of their targets [3, 4]
We present the miRBaseConverter R package to provide a suite of functions for querying miRNA name, accession, sequence, species, version and family information in different versions of miRBase
The miRBaseConverter package implemented in R is designed for the miRNA research community to assist with converting and retrieving miRNA information in different versions of miRBase. miRBaseConverter provides a suite of functions for querying miRNA name, accession, sequence, species, version and family information

Summary

Introduction

MicroRNAs (miRNAs) are short non-coding RNA molecules (about 22 nucleotides) that are widely encoded by eukaryotic nuclear DNA in plants and animals, and by viral DNA in some viruses [1, 2]. miRNAs are one of the vital and evolutionarily molecules that play an important role in post-transcriptional regulation by promoting degradation and repressing translation of their targets [3, 4]. MiRBase (http://www.mirbase.org/) is the home of miRNA data by providing a centralized system for assigning names and unique gene IDs for novel miRNAs [8,9,10]. It has become a primary repository of miRNA annotations and sequences for all species, a complete database of miRNA information, and the official rules for miRNA nomenclature. MiRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses

Results

Discussion

Conclusion