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||3029|
|Curated GO terms||4178|
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.
New batch download options added.
October 26, 2015
Removed 11 genomes with assemblies marked as 'suppressed' by NCBI. Many of these suppressed assemblies had flags indicating problems with assembly (More).
Reloaded RefSeq genomes with updated assemblies to fix problem with some sequence files being missing.
September 28, 2015
129 updates including new genes, product names, and subcellular localizations.
38 manually annotated GO terms
New isolates. Added 619 complete and draft Pseudomonas genomes downloaded from NCBI RefSeq.
Updated virulence factor annotations to provide more contextual information
Curated isolate metadata for isolation source, host organism, host disease status and geographical information.
Downloads page updated. Provided links to GTF files containing intergenic regions and genes. The format of the sequence headers in the corresponding fasta files have been slightly adjusted to match the sequence identifiers in the GTF files.
Fixed bug that was causing pseudogenes to not be shown in linear gene plots.
September 17, 2015
Links to details about intergenic regions have been returned to the gene details images. We have enhanced this feature to include the ability to change the amount of region displayed (e.g. look further upstream into a gene, look further downstream, etc.).
Added links to the motifs to allow searching for more occurences (e.g. search for more occurences of a TF binding site).
BlastN search results and DNA Motif search results now contain a link to show all hits (highlighted in bold boxes) in context of their surrounding genes. To do this, simply click on the "Genomic Context" link under each matching sequence.
Made some configuration changes to address server lag and downtime experienced yesterday and today.
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.