Strain-Specific Summaries and Analyses
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Submit an update to the continually-updated Pseudomonas aeruginosa PAO1 or LESB58 genome annotations.
DNA/Amino Acid Sequences
Retrieve a specific range from genomic DNA.
Download a specific ORF's DNA or protein sequence.
Pseudomonas Genome Projects - A summary of complete and in-progress sequencing projects.
Pseudomonas Genome Database updates and moreFollow @pseudocap
Since 2001, the Pseudomonas Genome database has been a resource for peer-reviewed, continually-updated annotations for the Pseudomonas aeruginosa PAO1 reference strain's genome and, more recently, comparative analyses of several related Pseudomonas species.
April 14, 2014
Annotation files are now available for download in GFF3 format.
April 11, 2014
Ortholog download files have been updated to fix issue where some orthologs were missing.
January 29, 2014
44 updates including new genes, product names, PseudoCAP functional classifications and references were added to the P. aeruginosa PAO1 genome annotation.
1994 manually-curated gene ontology (GO) term annotations added to P. aeruginosa PAO1, of which 1042 have been experimentally demonstrated in P. aeruginosa.
Curated GO term annotations transferred to conservative Pseudomonas Ortholog Group (POG) orthologs in other P. aeruginosa strains.
New search form: Browse PseudoCAP-curated GO terms.
Curated GO term annotations for P. aeruginosa strains can now be downloaded in gaf version 2.0 format.
Fixed bug where GO term (but not GO accession) searches were returning 0 results.
November 6, 2013
30 updates including new genes, product names, PseudoCAP functional classifications and references were added to the P. aeruginosa PAO1 genome annotation.
112 manually curated Gene Ontology (GO) terms mapped to 129 genes.
Added curations for the agtABCD, agtSR and magABCDEF operons.
Updated analysis of Pseudomonas proteins having greater than 90% identity to proteins with known 3D structures in the RCSB Protein Data Bank. Updated database of PDB sequences of proteins with known 3D structure.
Updated list of Pseudomonas proteins having human homologs (based on Ensembl release 73).
September 3, 2013
Amino acid sequences for genes containing atypical start codons (e.g. GTG TTG) were missing the initial methionine. This has been addressed and the database download files, gene records and BLAST databases have been updated with the correct sequences.
The PseudoCAP functional classifications assigned to P. aerugionsa PA14 were inadvertently dropped during the August 1, 2013 annotation update. They have been reassigned to their respective genes and the annotation files available for download have been updated.
August 1, 2013
Updated analysis identifying pathogen-associated genes in 9 Pseudomonas strains annotated as being pathogenic (more details).
Added complete genome sequences and annotations for 12 recently sequenced Pseudomonas strains for a total of 48 genomes in this database. In the Genome Projects Overview, added ability to toggle between all Pseudomonas Genomes and only those found in the database.
Updated Conserved Domain Database predictions based on CDD Version 3.10 [21 MAR 2013] from NCBI.
April 4, 2013
33 annotation updates to P. aeruginosa PAO1 genome.
350 specific Gene Ontology (GO) terms manually mapped to 129 Class 1 proteins from the "Transcriptional Regulators" function class. Started process of linking individual references to each curated GO term. For example, go to gene card for rpoS and click on the "Function/Structure" tab to see curated GO terms.
Gene cards contain new links to OrtholugeDB. From this link, you can access a comprehensive list of predicted orthologs, in-paralogs, pre-computed ortholog groups and other analyses in bacterial and archaeal strains.
Our lab's IslandViewer software for the computational identification and visualization of genomic islands has been updated. It's now possible to view annotations for virulence factor, antibiotic resistance and pathogen-associated genes on top of predictions for genomic islands. For example view the predictions for P. aeruginosa PAO1 or access others from the Browse Genomic Islands Using IslandViewer form on the "Browse Annotations" page.
March 8, 2013
2 annotation updates updates to P. aeruginosa PAO1 genome.