Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Centre for Systems Medicine, Dublin 2, Ireland.
Bioinformatics. 2017 Feb 15;33(4):592-593. doi: 10.1093/bioinformatics/btw660.
The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter , available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results.
The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor ( http://bioconductor.org/packages/miRNAmeConverter ). The web interface is based on R Shiny and can be accessed under the URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/ . The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor ( http://bioconductor.org/packages/miRBaseVersions.db ). Minimum R version 3.3.0 is required.
Supplementary data are available at Bioinformatics online.
miRBase 数据库是 miRNA 的中心和官方存储库，当前版本是 miRBase 版本 21.0。不同 miRBase 版本中的名称更改导致 miRNA 名称在版本之间不一致。在处理少量 miRNA 时，可以手动进行翻译。但是，对于大量 miRNA，对这种不一致性进行必要的修正变得繁琐且容易出错。我们开发了 miRNAmeConverter，它可用作 Bioconductor R 包和 Web 界面，用于解决成熟 miRNA 名称不一致相关的挑战。实现的主要算法支持高通量自动将物种独立的成熟 miRNA 名称转换为用户选择的 miRBase 版本。Web 界面使不太熟悉 R 的用户能够翻译以列表形式或嵌入文本中的 miRNA 名称，并下载结果。
miRNAmeConverter R 包在 Artistic-2.0 许可证下是开源的。它可以从 Bioconductor（http://bioconductor.org/packages/miRNAmeConverter）免费获得。Web 界面基于 R Shiny，可以通过 URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/访问。miRNAmeConverter 所依赖的数据库由注释包 miRBaseVersions.db 提供，可从 Bioconductor（http://bioconductor.org/packages/miRBaseVersions.db）下载。最低 R 版本 3.3.0 是必需的。
补充数据可在 Bioinformatics 在线获得。
