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Mining the Pseudomonas Genome

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Pseudomonas Methods and Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1149))

Abstract

Pseudomonas species were targeted early for genomic studies since they were noted for their diverse metabolic capacity, ability to inhabit a wide range of environments and hosts, and include notable human and agriculturally relevant pathogens. As more genomes are sequenced, the power of genome-scale analyses are increasing and a wide range of analyses are now possible. The Pseudomonas Genome database has contributed to this effort by providing peer-reviewed, continually updated annotations of the Pseudomonas aeruginosa PAO1 reference strain genome plus integrated data and analyses of related Pseudomonas species. Analyses are now available via multiple resources to facilitate identification and characterization of drug targets, virulence factors, regulatory elements, genomic islands, genome rearrangements, orthologs, single nucleotide polymorphisms, and multiple other gene/protein-based analyses from gene expression to protein structure. We describe here how the Pseudomonas Genome Database and other bioinformatics resources can be leveraged to help Pseudomonas researchers “mine” Pseudomonas genomes, and associated genome-scale data, to facilitate new discovery.

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Acknowledgment

We wish to acknowledge the efforts of the many genome sequencing projects and Pseudomonas researchers that have made our analysis possible. FSLB is a Michael Smith Foundation for Health Research (MSFHR) Senior Scholar. Critical funding was provided by Cystic Fibrosis Foundation Therapeutics.

Author information

Authors and Affiliations

  1. Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6

    Geoffrey L. Winsor & Fiona S. L. Brinkman

Authors
  1. Geoffrey L. Winsor
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  2. Fiona S. L. Brinkman
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Corresponding author

Correspondence to Fiona S. L. Brinkman .

Editor information

Editors and Affiliations

  1. MRC Centre for Molecular Bacteriology and Infection (CMBI) Department of Life Sciences, Imperial College, London, UK

    Alain Filloux

  2. Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain

    Juan-Luis Ramos

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© 2014 Springer Science+Business Media New York

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Winsor, G.L., Brinkman, F.S.L. (2014). Mining the Pseudomonas Genome. In: Filloux, A., Ramos, JL. (eds) Pseudomonas Methods and Protocols. Methods in Molecular Biology, vol 1149. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-0473-0_33

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  • DOI: https://doi.org/10.1007/978-1-4939-0473-0_33

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-0472-3

  • Online ISBN: 978-1-4939-0473-0

  • eBook Packages: Springer Protocols

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