Related Links

Additional resources for Pseudomonas aeruginosa sequence analysis, gene annotation and functional pathway analysis are listed below. We encourage researchers to contact us with suggestions for additional items that should be listed.


Other Pseudomonas species genome annotations

 

Pseudomonas genome project lists - including those in progress


Pseudomonas aeruginosa Transposon Mutant Library Databases


Other analyses

  • Pseudomonas aeruginosa PAO1 Protein Interactome - Based on the following publication:

    Zhang M, Su S, Bhatnagar RK, Hassett DJ, Lu LJ. Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PLoS One. 2012;7(7):e41202. Epub 2012 Jul 24. PubMed PMID: 22848443; PubMed Central PMCID: PMC3404098.

    A website available at http://research.cchmc.org/PPIdatabase/index.html hosts the data and details of the analysis. It provides an interface to enter a protein of interest and view a list of predicted interactions.

  • oprD, oprI, oprL allele data - Jean-Paul Pirnay, Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels Belgium.

    Sequenced from a collection of 328 diverse P. aeruginosa strains isolated by 69 institutes in 30 countries (5 continents), from diverse sources (river , pond and sea water, plants, animals and human CF, burns etc.) between 1882-2007.

    Download text file: oprD, oprI, oprL

  • IslandPath analyses for Pseudomonas aeruginosa (PAO1), P.syringae (DC3000, B728A, 1448A), P. fluorescens (Pf-5, PfO-1) and P.putida (KT2440)

    IslandPath is a graphical tool that aids with identification of genomics islands, including pathogenicity islands, of potentially horizontally transferred genes. Brinkman lab, Simon Fraser University, Burnaby, BC.

  • IslandViewer - Brinkman Lab, Simon Fraser University, Canada

    IslandViewer is tool for visualization of genomic islands that have been predicted using three different computational methods (IslandPick, SIGI-HMM and IslandPath-DIMOB).

  • WebACT - Imperial College, London.

    WebACT provides a database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool (ACT) developed by the Sanger Institute. Abbott JC, Aanensen DM, Bentley SD. 2007 (Pubmed)

  • Ribonucleotide reductase database (RNRdb). Department of Molecular Biology, Stockholm University, Stockholm, Sweden.

  • Potential human homologs (simple top BLAST hit to human proteins) of Pseudomonas aeruginosa PAO1 proteins. Brinkman lab, Simon Fraser University, Burnaby, BC.
  • Genome Atlas - Oak Ridge National Laboratory, Oak Ridge, TN, USA
  • ERGO Integrated Genomics, Inc., Chicago, Illinois, USA

Pathway or Function-Specific Annotations:
(annotations incorporated into original annotation - may or may not be updated)
  • Alginate Genes Kalai Mathee, Department of Biological Sciences, Florida International University, Miami, Florida, USA; Department of Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
  • Outer Membrane Proteins Robert E.W. Hancock, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada

Meetings


Other Related Databases

  • For those interested in pathogens of relevance to Cystic Fibrosis, note that a sister database for Burkholderia has been recently created. You can access it at burkholderia.com.