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The Use of ClusterMine360 for the Analysis of Polyketide and Nonribosomal Peptide Biosynthetic Pathways

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Nonribosomal Peptide and Polyketide Biosynthesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1401))

Abstract

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.

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Acknowledgements

This work has been supported by NSERC and an Early Researcher Award from the Province of Ontario.

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Authors and Affiliations

  1. Department of Chemistry and the Center for Advanced Research on Environmental Genomics, University of Ottawa, Ottawa, ON, Canada, K1N 6N5

    Nicolas Tremblay, Kyle R. Conway & Christopher N. Boddy

  2. Department of Biology and the Center for Advanced Research on Environmental Genomics, University of Ottawa, Ottawa, ON, Canada, K1N 6N5

    Patrick Hill & Christopher N. Boddy

Authors
  1. Nicolas Tremblay
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  2. Patrick Hill
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  3. Kyle R. Conway
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  4. Christopher N. Boddy
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Corresponding author

Correspondence to Christopher N. Boddy .

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Editors and Affiliations

  1. Donald Danforth Plant Science Center, Saint Louis, Missouri, USA

    Bradley S. Evans

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Tremblay, N., Hill, P., Conway, K.R., Boddy, C.N. (2016). The Use of ClusterMine360 for the Analysis of Polyketide and Nonribosomal Peptide Biosynthetic Pathways. In: Evans, B. (eds) Nonribosomal Peptide and Polyketide Biosynthesis. Methods in Molecular Biology, vol 1401. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3375-4_15

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  • DOI: https://doi.org/10.1007/978-1-4939-3375-4_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3373-0

  • Online ISBN: 978-1-4939-3375-4

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