Microorganisms produce secondary metabolites with a remarkable range of bioactive properties. The constantly increasing amount of published genomic data provides the opportunity for efficient identification of biosynthetic gene clusters by genome mining. On the other hand, for many natural products with resolved structures, the encoding biosynthetic gene clusters have not been identified yet. Of those secondary metabolites, the scaffolds of nonribosomal peptides and polyketides (type I modular) can be predicted due to their building block-like assembly. SeMPI v2 provides a comprehensive prediction pipeline, which includes the screening of the scaffold in publicly available natural compound databases. The screening algorithm was designed to detect homologous structures even for partial, incomplete clusters. The pipeline allows linking of gene clusters to known natural products and therefore also provides a metric to estimate the novelty of the cluster if a matching scaffold cannot be found. Whereas currently available tools attempt to provide comprehensive information about a wide range of gene clusters, SeMPI v2 aims to focus on precise predictions. Therefore, the cluster detection algorithm, including building block generation and domain substrate prediction, was thoroughly refined and benchmarked, to provide high-quality scaffold predictions. In a benchmark based on 559 gene clusters, SeMPI v2 achieved comparable or better results than antiSMASH v5. Additionally, the SeMPI v2 web server provides features that can help to further investigate a submitted gene cluster, such as the incorporation of a genome browser, and the possibility to modify a predicted scaffold in a workbench before the database screening.

中文翻译：

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SeMPI 2.0-用于PKS和NRPS预测的Web服务器，结合天然产物数据库中的代谢物筛选

微生物产生具有广泛生物活性的次级代谢产物。不断增加的已发布基因组数据数量为通过基因组挖掘有效识别生物合成基因簇提供了机会。另一方面，对于许多具有解析结构的天然产物，尚未鉴定出编码的生物合成基因簇。在这些次级代谢产物中，非核糖体肽和聚酮（I型模块）的支架由于其构建块状组装而可以预测。SeMPI v2提供了全面的预测流程，其中包括在可公开获得的天然化合物数据库中筛选支架。筛选算法旨在检测同源结构，即使是部分不完整的簇。流水线允许将基因簇链接到已知的天然产物，因此，如果找不到匹配的支架，还可以提供一种度量来评估簇的新颖性。当前可用的工具试图提供有关广泛基因簇的全面信息，而SeMPI v2则致力于精确的预测。因此，对聚类检测算法（包括构件生成和域底物预测）进行了彻底的完善和基准测试，以提供高质量的支架预测。在基于559个基因簇的基准测试中，SeMPI v2取得了与antiSMASH v5相当或更好的结果。此外，SeMPI v2网络服务器还提供了有助于进一步调查提交的基因簇的功能，例如整合了基因组浏览器，