NEWS

July 29, 2010

253 annotation updates.

Important Update - New ability to view SNPs/small indels between strains of same species. We currently have this feature implemented for the reference strain Pseudomonas aeruginosa PAO1, whereby SNPs and indels identified by specific studies or whole-genome alignment (e.g. P. aeruginosa 2192) have been identified. SNPs occurring in coding regions are currently identified under the "polymophisms" tab on gene pages (example) but we soon plan to expand the scope to include non-coding regions. Please send any suggested improvements or comments on this new feature to pseudocap-mail@sfu.ca.

Genome summary pages now include links to the NCBI Trace Archive as well as summaries of experiments from EBI ArrayExpress and NCBI Gene Expression Omnibus.

Gene cards now feature tabbed browsing for easier navigation.

Updated the list of completed and incomplete genome sequencing projects in the list of Pseudomonas genome projects.

Fixed issue with some duplicate subcellular localization classifications being returned

Some downloadable text files had formatting errors (e.g. line breaks) that have been corrected

Updated all external (i.e. not PAO1 or LESB58) genome annotations using NCBI RefSeq genome annotations available as of 2010-07-02.

March 11, 2010

Tool for downloading search results has been updated in order to increase speed of download for large result lists and allow easier parsing of text. As a result, column format has changed.

February 1, 2010

Genome summary pages now include more detailed information and links for downloading data.

New batch download feature: Ability to download high-precision ortholog predictions from links in genome menu pages (e.g. Orthologs under "Download" tab of PAO1 menu) as well as the main downloads page.

Transposon library data for the Pseudomonas aeruginosa PAO1 (MPAO1) two-allele library has been updated in GBrowse. The Two-allele library was created as a subset of the original library and where possible, contains single colony purified isolates of two alleles of each PA ORF insertion.

New analyses in GBrowse. Computationally-predicted Rho-independent terminators (TransTermHP) and palindromes (EMBOSS). Click here to view an example.

Reference sections of gene summary pages now contain full literature citations (previously included just the PMID).

Gene cards for Pseudomonas aeruginosa PAO1 genes now have links to gene specific NCBI GEO Microarray Expression Data.

The navigation bar now includes drop down menus.

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Pseudomonas aeruginosa is a versatile Gram-negative bacterium that grows in soil, coastal marine habitats, and on plant and animal tissues. People with cystic fibrosis, burn victims, and other patients in intensive care units are particularly at risk of disease resulting from P. aeruginosa infection. The complete sequence of the genome of P. aeruginosa strain PAO1 was published in Nature in the year 2000 and was noted for its large size and diverse metabolic capacity. The genome annotation is now being continually updated and the database functionality is being expanded to facilitate accelerated discovery of P. aeruginosa drug targets and vaccine candidates. This effort is being co-ordinated by Dr. Fiona Brinkman at Simon Fraser University and Dr. Bob Hancock at the University of British Columbia with database development led by Geoff Winsor of the Brinkman group. 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. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP participating researchers. If you are interested in participating, we invite you to get involved. Note that as of 2005, this database now also provides data on other Pseudomonas species genomes, which acts as a valuable comparative resource for P. aeruginosa research, as well as being useful for the larger Pseudomonas research community. We aim to continue to provide a central portal through which researchers may access high quality genome-associated information about P. aeruginosa and potential drug/vaccine targets, helping to accelerate research efforts to control important Pseudomonas infections.

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We thank Cystic Fibrosis Foundation Therapeutics, Inc (CFFT) for critical funding support for the Pseudomonas Genome Database.



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Pseudomonas aeruginosa

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