The Pseudomonas Genome Database collaborates with an international panel of expert Pseudomonas researchers to provide high quality updates to the PAO1 genome annotation and make cutting edge genome analysis data available
|Manually-curated annotation updates||4006|
|Curated GO terms||4140|
View Complete and Draft Genomes
You can now view annotations and sequences for both complete and draft genomes.
|View a list of complete and draft Pseudomonas genomes in this database:|
|Pseudomonas genome, transcriptome and epigenomic projects at NCBI:|
|Updates to gene annotations in this database:|
We welcome all suggested updates to Pseudomonas annotations and no registration is required!
PseudoCAP was the first wholly Internet-based and community-based genome annotation project for analysis of a genome of a free-living organism.
Funding for this work is gratefully provided by Cystic Fibrosis Foundation Therapeutics Inc., a non-profit drug discovery and development affiliate of the Cystic Fibrosis Foundation.
August 31, 2015 (1)
Service restored after lengthy power outage on SFU campus. Power to much of SFU campus was disrupted at 12:00 pm PDT on Saturday, August 29 and negatively impacted campus IT services and the Pseudomonas Genome Database website throughout the weekend. Thanks for your patience during this time.
August 31, 2015 (2)
We have received feedback from users on how they would like intergenic region annotations to be viewed (e.g. similar to how they were on the older version of the site). A solution is being prepared for the near future that will take these suggestions into consideration.
For now, gene details pages will contain annotations for upstream and downstream intergenic regions under the "motifs" tab. For example, when you are viewing a gene such as oprF.
We also provide JBrowse and GBrowse links from gene details pages. These will bring you to a visual representation of the intergenic annotations which you can click on for more information (example). Please feel free to contact us and send any further suggestions.
August 25, 2015
The latest version of the Pseudomonas Genome Database has left beta status and gone live. While the old site has been retired and is not being updated, it will be available for a short time at v2.pseudomonas.com.
July 31, 2015
Fixed issue with server error occurring when querying proteins by subcellular localization. Enhanced speed of subcellular localization search as well.
June 11, 2015
Evidence of translation provided for 2965 P. aeruginosa PAO1 proteins based on HPLC-MS data from Kumari et al.(2014).
Fixed bug that was causing some recently added PubMed references to not appear.
June 10, 2015
23 updates including new proteins identified using nanoflow high-pressure liquid chromatography (HPLC) in conjunction with microelectrospray ionization on LTQ XL mass spectrometer. Genomic coordinates reannotated for some ORFs based on RT-PCR evidence.
May 21, 2015
Optimized time it takes to download ortholog data from the Orthologs page (under "Annotations By Category"). Posted new links to pre-generated ortholog files on the downloads page. Data for more strains will become available when our Pseudomonas Ortholog Group (POGs) and Ortholuge analyses are updated in a few weeks.
May 19, 2015
Fixed broken download option for Blast search results. Clicking on link to download results in CSV,Excel,PDF,ODS or RTF format was returning ERR_INVALID_RESPONSE but now gives expected result.
Added links to download raw Blast results in tab-delimited (-outfmt 6) and pairwise aligment (-outfmt 0) formats.
May 14, 2015
Fixed bug in search forms where query strain was sometimes not being reset when the input box was cleared by user.
May 12, 2015
Official release of 4118 manually-curated GO term annotations in which a majority (3457) belong to P. aeruginosa PAO1 and are derived from the Pseudomonas GO annotation initiative performed last year. A manuscript describing the community-based GO biocuration initiative is in preparation, however in the interest of open data we are releasing the annotations in advance of publication.
May 12, 2015
We are pleased to announce the beta release of a new and improved Pseudomonas Genome Database containing annotations, sequences and metadata for hundreds of Pseudomonas genomes.
New features associated with this version include:
1) Expanded capability to view sequences and annotations for 939 complete AND draft genomes with more coming very soon!
2) Improved tracking of strain/isolate metadata.
3) New and updated annotations including high quality virulence factor annotations and manually annotated GO term updates.
4) New whole-genome computational analyses including the identification of pathogen-associated genes, proteins with 3D structures, subcellular localization predictions, functional domain mappings and biological pathway predictions.
5) Integration of new genome browser (JBrowse) with features well suited for viewing your own genome annotations (e.g. alternate gene annotations, quantitative data, RNA-Seq data, variant data). Note: We are also still maintaining GBrowse for those that still prefer to use it.
141 updates including new genes, product names, PseudoCAP functional classifications and references were added.
March 6, 2015
Added virulence factor annotations obtained from the PHIDIAS Victors database.
February 19, 2015
Added high quality annotations for 1143 transcription factor binding sites obtained from the CollecTF database.
December 1, 2014
233 updates including new genes, product names, PseudoCAP functional classifications and references were added.
Updated the links page.