Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC's data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others') through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

中文翻译：

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次生代谢合作室：次生代谢物生物合成基因簇的数据库和网络讨论门户。


次生代谢物是生命各个角落产生的小分子，通常具有具有临床和环境相关性的特殊生物活性功能。次生代谢物生物合成基因簇 （BGC） 通常可以通过各种序列相似性工具在 DNA 序列中识别，但确定基因在通路中的确切功能并预测其化学产物通常只能通过仔细的手动比较分析来完成。为了促进这一点，我们报告了次级代谢合作室 （SMC） 的第一个版本，该版本旨在提供一个全面的、与工具无关的 BGC 序列数据存储库，这些数据来自所有公开可用和用户提交的细菌和古细菌基因组和重叠群来源。在该网站上，为用户提供了从每个来源识别的推定 BGC 的可搜索目录，以及来自多个序列分析工具的基因和结构域注释的可视化。SMC 的数据还可以通过可公开访问的应用程序编程接口 （API） 端点获得，以方便以编程方式访问。鼓励用户通过 BGC 和源页面上的评论帖子分享他们的发现（并搜索其他人的发现）。在撰写本文时，SMC 是最大的 BGC 信息存储库，拥有来自 1.3M 源序列的 13.1M BGC 区域，并且还在不断增长，可以在 https://smc.jgi.doe.gov 找到。