Mining the Pseudomonas genome

Methods Mol Biol. 2014;1149:417-32. doi: 10.1007/978-1-4939-0473-0_33.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Mining*
  • Databases, Genetic
  • Gene Expression Regulation, Bacterial
  • Gene Rearrangement
  • Genes, Bacterial
  • Genome, Bacterial / genetics*
  • Genomic Islands / genetics
  • Genomics / methods*
  • Humans
  • INDEL Mutation / genetics
  • Molecular Sequence Annotation
  • Multigene Family
  • Nucleotide Motifs / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Pseudomonas / genetics*
  • Pseudomonas / pathogenicity
  • Software
  • Subcellular Fractions / metabolism
  • User-Computer Interface
  • Virulence / genetics