使用ClusterMine360分析聚酮化合物和非核糖体肽生物合成途径。
The Use of ClusterMine360 for the Analysis of Polyketide and Nonribosomal Peptide Biosynthetic Pathways.
作者信息
Tremblay Nicolas, Hill Patrick, Conway Kyle R, Boddy Christopher N
机构信息
Department of Chemistry and the Center for Advanced Research on Environmental Genomics, University of Ottawa, Ottawa, ON, Canada, K1N 6N5.
Department of Biology and the Center for Advanced Research on Environmental Genomics, University of Ottawa, Ottawa, ON, Canada, K1N 6N5.
出版信息
Methods Mol Biol. 2016;1401:233-52. doi: 10.1007/978-1-4939-3375-4_15.
Polyketides and nonribosomal peptides constitute two large families of microbial natural products. Over the past 20 years a broad range of microbial polyketide and nonribosomal peptide biosynthetic pathways have been characterized leading to a surfeit of genetic data on polyketide and nonribosomal peptide biosynthesis. We developed the ClusterMine360 database, which stores the antiSMASH-based annotation of gene clusters in the NCBI database, linking the structure of the natural product to the biosynthetic gene cluster. This database is searchable and enables the user to access multiple sequence files for phylogenetic analysis of polyketide and nonribosomal peptide biosynthetic genes. Herein we describe how to add compound families and gene clusters to the database and search it using key words or structures to identify specific gene clusters. We also describe how to download multiple sequence files for specific catalytic domains from polyketide and nonribosomal peptide biosynthesis.
聚酮化合物和非核糖体肽构成了微生物天然产物的两大类别。在过去20年里，大量微生物聚酮化合物和非核糖体肽的生物合成途径已得到表征，产生了关于聚酮化合物和非核糖体肽生物合成的大量遗传数据。我们开发了ClusterMine360数据库，该数据库存储了基于antiSMASH对NCBI数据库中基因簇的注释，将天然产物的结构与生物合成基因簇联系起来。该数据库可搜索，用户能够访问多个序列文件，用于聚酮化合物和非核糖体肽生物合成基因的系统发育分析。在此，我们描述如何向数据库中添加化合物家族和基因簇，以及如何使用关键词或结构搜索数据库以识别特定的基因簇。我们还描述了如何从聚酮化合物和非核糖体肽生物合成中下载特定催化结构域的多个序列文件。
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