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.

Pseudomonas genome projects at NCBI BioProject

View a list of genome and transcriptome projects in this database.

View a list at the Genomes Online website

View listing of complete and incomplete microbial genome projects at NCBI.

Transposon Mutant Library Databases

Pseudomonas aeruginosa PAO1 mini-Tn5 lux transposon mutant library (developed by the Hancock Laboratory, UBC)


Pseudomonas aeruginosa PAO1 phoA/lacZ transposon library generated by the University of Washington Genome Centre


Pseudomonoas aeruginosa PA14 non-redundant transposon insertion library developed by Ausubel lab at Harvard Medical School.


HoPaCI-DB: host-Pseudomonas and Coxiella interaction database

The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii.

Website

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

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

Hosted by the Brinkman Lab, Simon Fraser University, Canada

IslandViewer Website

WebACT

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)

Hosted by Imperial College, London. (website)

Ribonucleotide reductase database (RNRdb)

Department of Molecular Biology, Stockholm University, Stockholm, Sweden. (website)

Other analyses

Genome-scale collection of Pseudomonas ORFs in recombinational cloning vectors - Harvard Institute of Proteomics at Harvard Medical School.

PseuRECA (Pseudomonas REannotation and Context Analysis) - Klinische Forschergruppe, Hannover, Germany; The European Bioinformatics Institute (EMBL), Cambridge , UK; The Institute for Genomic Research, Rockville, MD , USA

NCBI's Pseudomonas aeruginosa genome information - National Center for Biotechnology Information, Bethesda, Maryland, USA

Genome Atlas - Oak Ridge National Laboratory, Oak Ridge, TN, USA

Microbial Genome Database for Comparative Analysis - University of Tokyo, Tokyo, Japan

NCBI BLAST against Pseudomonas aeruginosa, Pseudomonas putida, and others - National Center for Biotechnology Information, Bethesda, Maryland, USA

Search PubMed for recent Pseudomonas aeruginosa-related publications - National Center for Biotechnology Information, Bethesda, Maryland, USA

KEGG: Kyoto Encyclopedia of Genes and Genomes Minoru Kanehisa, Institute for Chemical Research, Kyoto University, Kyoto, Japan

ERGO Integrated Genomics, Inc., Chicago, Illinois, USA

Codon Usage Database - Pseudomonas aeruginosa - Yasukazu Nakamura, First Laboratory for Plant Gene Research, Kazusa DNA Research Institute, Chiba, Japan

Pseudomonas Genomes at PEDANT - Dmitrij Frishman, Munich Information Center for Protein Sequences, Am Klopferspitz, Germany

PRODORIC: Prokaryotic Database of Gene Regulation and Regulatory Networks (includes P. aeruginosa regulons) - Technical University of Braunschweig, Braunschweig, Germany


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

Genetic Comparisons of Membrane Transport Systems Ian Paulsen, The Institute for Genomic Research, Rockville, Maryland, USA

Outer Membrane Proteins Robert E.W. Hancock, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada


Meetings

ASM Conference on Pseudomonas - Seattle, Washington, USA (August 26-30, 2007).


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.


Other Pseudomonas species genome annotations

Pseudomonas aeruginosa PA14 genome sequencing project home page - Massachusetts General Hospital, Harvard Medical School

Pseudomonas aeruginosa PA7 genome page - J. Craig Venter Institute (JCVI), Microbial Sequencing Center (MSC)

Pseudomonas fluorescens Pf-5 genome page - Institute for Genomic Research (TIGR)

Pseudomonas fluorescens PfO-1 genome page - DOE Joint Genome Institution (JGI), The Regents of the University of California

Pseudomonas mendocina ymp genome page - DOE Joint Genome Institution (JGI), The Regents of the University of California

Pseudomonas putida F1 genome page - DOE Joint Genome Institution (JGI), The Regents of the University of California

Pseudomonas putida KT2440 genome page - Institute for Genomic Research (TIGR)

Pseudomonas stutzeri A1501 - While this link is to the annotation at NCBI, the sequencing centers are The Biotechnology Research Institute and The Chinese Academy of Agricultural Sciences. Annotation has not been added to the web site yet.

Pseudomonas syringae DC3000 annotation project - Browse the current annotation for Pseudomonas syringae DC3000 using the Artemis genome viewer. Includes a portal for submitting annotation updates and viewing its annotation at NCBI.

Pseudomonas syringae B728a annotation project - Browse the current annotation for Pseudomonas syringae B728a using the Artemis genome viewer. Includes a portal for submitting annotation updates and viewing its annotation at NCBI.

Pseudomonas syringae phaseolicola 1448A annotation project - Browse the current annotation forPseudomonas syringae phaseolicola using the Artemis genome viewer. Includes a portal for submitting annotation updates and viewing its annotation at NCBI.

Also see our acknowledgements page