Hendling Michaela, Conzemius Rick, Barišić Ivan
Austrian Institute of Technology, Center for Health & Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210 Vienna, Austria.
Comput Struct Biotechnol J. 2021;19:847-851. doi: 10.1016/j.csbj.2021.01.024. Epub 2021 Jan 19.
The amount of publicly available DNA sequence data is drastically increasing, making it a tedious task to create sequence databases necessary for the design of diagnostic assays. The selection of appropriate sequences is especially challenging in genes affected by frequent point mutations such as antibiotic resistance genes. To overcome this issue, we have designed the webtool resiDB, a rapid and user-friendly sequence database manager for bacteria, fungi, viruses, protozoa, invertebrates, plants, archaea, environmental and whole genome shotgun sequence data. It automatically identifies and curates sequence clusters to create custom sequence databases based on user-defined input sequences. A collection of helpful visualization tools gives the user the opportunity to easily access, evaluate, edit, and download the newly created database. Consequently, researchers do no longer have to manually manage sequence data retrieval, deal with hardware limitations, and run multiple independent software tools, each having its own requirements, input and output formats. Our tool was developed within the H2020 project FAPIC aiming to develop a single diagnostic assay targeting all sepsis-relevant pathogens and antibiotic resistance mechanisms. ResiDB is freely accessible to all users through https://residb.ait.ac.at/.
公开可用的DNA序列数据量正在急剧增加，这使得创建诊断检测设计所需的序列数据库成为一项繁琐的任务。在受频繁点突变影响的基因（如抗生素抗性基因）中选择合适的序列尤其具有挑战性。为了克服这个问题，我们设计了网络工具resiDB，这是一个快速且用户友好的序列数据库管理器，用于管理细菌、真菌、病毒、原生动物、无脊椎动物、植物、古细菌、环境和全基因组鸟枪法测序数据。它会自动识别和整理序列簇，以根据用户定义的输入序列创建自定义序列数据库。一系列有用的可视化工具让用户有机会轻松访问、评估、编辑和下载新创建的数据库。因此，研究人员不再需要手动管理序列数据检索、应对硬件限制以及运行多个各自有其要求、输入和输出格式的独立软件工具。我们的工具是在H2020项目FAPIC中开发的，该项目旨在开发一种针对所有与败血症相关的病原体和抗生素抗性机制的单一诊断检测方法。所有用户均可通过https://residb.ait.ac.at/免费访问ResiDB。
