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Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

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Nonribosomal Peptide and Polyketide Biosynthesis

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

Abstract

This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two-dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i.e., antibiotics against multi-resistant pathogens or anti-tumors).

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Acknowledgements

TW is supported by a grant of the Novo Nordisk Foundation. The work on Norine is supported by PPF Bioinformatique of Lille 1 University and Bilille.

We thank Hyun Uk Kim for testing the workflows and careful reading of the chapter.

Author information

Authors and Affiliations

  1. ProBioGEM, Institut Charles Viollette, Polytech’Lille, University of Lille 1, 59650, Villeneuve d’Ascq, France

    Valérie Leclère & Philippe Jacques

  2. CRIStAL, UMR 9189, Univ Lille, 59650, Villeneuve d’Ascq, France

    Valérie Leclère & Maude Pupin

  3. Inria Lille Nord-Europe, 59650, Villeneuve d’Ascq, France

    Valérie Leclère & Maude Pupin

  4. The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark

    Tilmann Weber

Authors
  1. Valérie Leclère
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  2. Tilmann Weber
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  3. Philippe Jacques
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  4. Maude Pupin
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Corresponding author

Correspondence to Maude Pupin .

Editor information

Editors and Affiliations

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

    Bradley S. Evans

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Leclère, V., Weber, T., Jacques, P., Pupin, M. (2016). Bioinformatics Tools for the Discovery of New Nonribosomal Peptides. 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_14

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  • DOI: https://doi.org/10.1007/978-1-4939-3375-4_14

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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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