Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy.
Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy.
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Taxonize-gb：一种根据分类法过滤GenBank非冗余数据库的工具。
DOI：
10.1101/2024.03.22.586347
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Fuchsberger,Christian
中科院分区：
文献类型：
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作者：
Sarhan,MohamedS;Filosi,Michele;Maixner,Frank;Fuchsberger,Christian
在不同的生态样本中分析分类多样性和鉴定已经成为各个研究和工业领域的重要常规。虽然DNA条形码标记基因方法曾经很流行，但下一代测序成本的下降已经使元基因组鸟枪测序变得更加流行和可行。与DNA条形码不同，元基因组鸟枪测序为深入表征结构和功能多样性提供了可能性。然而，由于缺乏特定于分类群的数据库，对这类数据的分析仍然被认为是一个障碍。在这里，我们介绍了Taxonize-GB，这是一个命令行软件工具，用于提取与一个或多个输入分类标识符相关的GenBank非冗余核苷酸和蛋白质数据库。我们的工具允许创建针对特定研究问题的特定于分类群的参考数据库，这减少了搜索时间，因此对于定期分析大型元基因组数据的研究人员来说，这是一个实用的解决方案。Taxonize-GB是一个开源的、基于PYTHON的命令行工具，可在https://pypi.org/project/taxonize-gb/和GitHub https://github.com/msabrysarhan/taxonize_genbank.上免费安装它是在知识共享署名-非商业4.0国际许可证(CC BY-NC 4.0)下发布的。
Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation at https://pypi.org/project/taxonize-gb/ and on GitHub https://github.com/msabrysarhan/taxonize_genbank. It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).