BCdatabaser：用于（元）条形码的实时参考数据库创建。

BCdatabaser: on-the-fly reference database creation for (meta-)barcoding.

机构信息

Center for Computational and Theoretical Biology, University of Würzburg, Hubland Nord, Würzburg 97074, Germany.

Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, Würzburg 97074, Germany.

出版信息

Bioinformatics. 2020 Apr 15;36(8):2630-2631. doi: 10.1093/bioinformatics/btz960.

DOI:10.1093/bioinformatics/btz960

PMID:31904820

Abstract

SUMMARY

DNA barcoding and meta-barcoding have become irreplaceable in research and applications, where identification of taxa alone or within a mixture, respectively, becomes relevant. Pioneering studies were in the microbiological context, yet nowadays also plants and animals become targeted. Given the variety of markers used, formatting requirements for classifiers and constant growth of primary databases, there is a need for dedicated reference database creation. We developed a web and command-line interface to generate such on-the-fly for any applicable marker and taxonomic group with optional filtering, formatting and restriction specific for (meta-)barcoding purposes. Also, databases optionally receive a DOI, making them well-documented with meta-data, publicly sharable and citable.

AVAILABILITY AND IMPLEMENTATION

source code: https://www.github.com/molbiodiv/bcdatabaser, webservice: https://bcdatabaser.molecular.eco, documentation: https://molbiodiv.github.io/bcdatabaser.

摘要

DNA 条码和元条码在研究和应用中已经变得不可或缺，分别在单独或在混合物中对分类单元进行鉴定变得至关重要。开创性的研究主要集中在微生物领域，但现在也涉及到植物和动物。鉴于所使用的标记物种类繁多，分类器的格式要求以及主要数据库的不断增长，因此需要创建专用的参考数据库。我们开发了一个网络和命令行界面，以便为任何适用的标记物和分类群生成实时数据库，并且可以选择进行（元）条码目的过滤、格式化和限制。此外，数据库可以选择接收 DOI，使其具有元数据文档、可公开共享和可引用。