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

Journal: BMC bioinformatics
Published Date: Dec 31, 2018

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.

Authors

  • Taosheng Xu
    Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
  • Ning Su
    Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
  • Lin Liu
    Institute of Natural Sciences, MOE-LSC, School of Mathematical Sciences, CMA-Shanghai, SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University; Shanghai Artificial Intelligence Laboratory.
  • Junpeng Zhang
    School of Engineering, Dali University, Dali, 671003, China.
  • Hongqiang Wang
    School of Electronic Science, National University of Defense Technology, Changsha 410073, China. wanghongqiang@nudt.edu.cn.
  • Weijia Zhang
  • Jie Gui
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, United States.
  • Kui Yu
    School of Computer and Information, Hefei University of Technology, Hefei, 230009, China.
  • Jiuyong Li
    School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia.
  • Thuc Duy Le
    School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095 Adelaide, Australia. Thuc.Le@unisa.edu.au.

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