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 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

Pseudomonas genome project lists - including those in progress

View our list of Pseudomonas genome projects

View a list at the Genomes Online website

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

Pseudomonas aeruginosa Transposon Mutant Library Databases

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

Pseudomonoas 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.

Other analyses

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.

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-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

Comprehensive Microbial Database - Pseudomonas aeruginosa - The Institute for Genomic Research, Rockville, Maryland, USA

WIT - Pseudomonas aeruginosa - Argonne National Laboratory, Argonne, Illinois, 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

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

EBI Computational Proteome Analysis - Pseudomonas aeruginosa - European Bioinformatics Institute, Welcome Trust Genome Campus, Cambridge, UK

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

A-Z Cystic Fibrosis Directory - Cell Science

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.