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BMC Bioinformatics. 2018 Dec 31;19(Suppl 19):514. doi: 10.1186/s12859-018-2531-5.

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

Author information

1
Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
2
School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095 Adelaide, Australia.
3
School of Engineering, Dali University, Dali, 671003, China.
4
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, United States.
5
National Engineering Research Center of Communications and Networking, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
6
School of Computer and Information, Hefei University of Technology, Hefei, 230009, China.
7
School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095 Adelaide, Australia. Thuc.Le@unisa.edu.au.
8
Centre for Cancer Biology, University of South Australia, SA, 5000 Adelaide, Australia. Thuc.Le@unisa.edu.au.

Abstract

BACKGROUND:

miRBase 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.

RESULTS:

We 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.

CONCLUSIONS:

The 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.

KEYWORDS:

Annotation; Bioinformatics; miRBase repository; miRNA; miRNA family; miRNA information retrieval

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