Please note that we will be retiring this old site on Tuesday, August 25th, 2015.
At that point, the URL for www.pseudomonas.com will bring you to our new site currently hosted at beta.pseudomonas.com. We encourage you to visit the new site now and see a more recent set of updated gene annotations and MANY more Pseudomonas strains.

Annotation Approach

The primary annotation of the Pseudomonas aeruginosa PAO1 genome was performed at PathoGenesis Corporation with the expert assistance of 81 scientists who were members of the P. aeruginosa research community or had experience in particular aspects of bacterial physiology. This project, the Pseudomonas aeruginosa Community Annotation Project (PseudoCAP), was organized by Dr. Robert Hancock and Dr. Fiona Brinkman of the University of British Columbia and Simon Fraser University, Canada. Now, as researchers use this genome sequence and its annotation to make new discoveries, this genome annotation is being continually updated, through a community-based approach being developed and supported by PseudoCAP and the Cystic Fibrosis Foundation.

Approach for primary Annotation of the P. aeruginosa PAO1 genome

The 5570 predicted ORFs were examined individually for homology with sequences in GenBank and for the presence of known functional motifs. Before assigning protein or gene names based on sequence similarity, we searched the literature for evidence that the function of the published gene had been demonstrated experimentally. Using this approach, we hoped to avoid the perpetuation of poorly supported functional assignments.

Each annotation includes a protein name confidence which reflects the type of evidence upon which the gene/protein name was based.

Protein Name Confidence 1: Function experimentally demonstrated in P. aeruginosa .

Protein Name Confidence 2: Function of highly similar gene experimentally demonstrated in another organism.

Protein Name Confidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology.

Protein Name Confidence 4: Homologs of previously reported genes of unknown function, or no homology to any previously reported sequences.

 

Approach for continual update of the genome annotation

For the continually updated genome annotation, updates will be performed on a continual basis with version numbers associated with each update (corresponding to the length of time between each update). Annotations will be subject to peer-review, with summaries of all updates proposed to be presented at the biannual International Pseudomonas meeting. It is also proposed that this meeting may serve as a suitable forum to address any issues regarding gene nomenclature, and other proposed changes to the genome annotation that may be more controversial over the years.

New annotations proposed by participating researchers were initially submitted by email, but as of the end of 2001 a new web-based form system was developed to facilitate annotation submissions. These forms allow for very flexible submissions depending on the type of submission made by the researcher. Authorship notations are also being included as database functionality expands, so that researchers who submit annotations can be appropriately acknowledged for their peer-reviewed contributions (see recent annotation updates). In addition, the database has also been further expanded, providing more query flexibility and more search fields for examination of the data. We hope that this approach to expanding the database functionality, continually updating annotations from the literature, and facilitating the inclusion of annotation updates by a community of researchers, will facilitate the development of a powerful and continually-useful central resource for the Pseudomonas research community.

For more information about submitting annotations for this project, see our description of how you can get involved.