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||3315|
|Curated GO terms||4365|
September 11, 2017
Fixed broken pathway download link that was always returning results for PAO1.
August 4, 2017
Fixed bug where some columns were missing from downloaded strain data files.
July 7, 2017
Maximum number of hits returned by DNA motif search tool has been increased from 2000 to 5000. Contact us by email for assistance with queries returning more than 5000 hits so that we can help you directly.
June 2, 2017
New release with 100 manually-curated annotation updates.
788 new Pseudomonas isolates and strains added to the database (view all strains).
Antibiotic resistance (AMR) gene predictions based on the Resistance Gene Identifier (RGI) analysis tool which utilizes the Comprehensive Antibiotic Resistance Database (CARD) hosted by Andrew McArthur's Lab at McMaster University. (PAO1 example)
Using annotations from DrugBank Version 5.0.5, we have identified 112,347 targets of 145 distinct drugs in Pseudomonas strains (PAO1 example).
New and faster alternative to BLASTP/BLASTX searches of protein databases. You can now use DIAMOND, which is thousands of times faster at searching protein sequence databases.
New functionality for downloading BLAST search results. Subject sequences aligned to query sequence OR complete subject sequences can now be downloaded in FASTA format. The aligned portions of query and subject sequences are also included as new columns in the CSV and Excel file downloads.
Links to updated genomic island predictions, virulence factors and AMR genes in IslandViewer 4. Simply go to a strain's replicon details page and follow the "View Genomic Islands in IslandViewer 4" link (e.g. PA14 replicon example)
Strains and Isolates in the 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.