- » Searching the database of genome annotations
- » Searching the log of annotation updates
- » Comparison of multiple annotations
- » Multiple alignment using ClustalW
- » BLAST search against other nucleotide and protein sequences in the database
- » How to identify orthologs in different strains/species
- » Locating orthologs from within a gene card
- » High-throughput identification and comparison of orthologs
- » How to Display and Configure Different GBrowse Tracks
- » New: How to upload and view RNA-Seq data in GBrowse
- » How to view polymorphisms in closely related strains
The Pseudomonas Genome database facilitates within-genome and multiple-genome comparison of annotations. In brief, the database includes the following major new features which are centered around aiding comparative analysis of Pseudomonas aeruginosa with other species.
- Search annotations associated with any Pseudomonas genome sequence who's annotations have been made available, versus just the Pseudomonas aeruginosa PAO1 genome.
- View and compare annotations within a Pseudomonas species (i.e. gene family) or between species.
- Perform multiple sequence alignments (DNA and protein) and BLAST-based searches using sequences specified during a comparison of multiple genes.
- Navigate between different species genomes and view alternate annotations using GBrowse.
- Customize GBrowse further to suit your needs (i.e. select and reorder annotation tracks).
- New: Upload and view RNA-Seq data in GBrowse.
- Under an individual gene view, you can view a graphic containing subcellular localization information for the protein associated with that gene, and there is an expanded list of links to other resources (more functional category information, links to other genome databases when suitable, etc.).
- Perform DNA Motif searches.
- View polymorphisms/SNPs in closely-related Pseudomonas genomes.
We emphasize that this database is still focused on the Pseudomonas aeruginosa PAO1 genome annotation and providing information of greatest relevance to Pseudomonas aeruginosa research. For other Pseudomonas species information we encourage you to examine the other excellent Pseudomonas genome databases available (see our links). For an individual gene view, we also provide a link to the associated annotation at other genome database sites, when possible.
We will be expanding the database further over the next year to include more information relevant to cystic fibrosis research and increased database flexibility. We encourage you to contact us with any features you would like to see in this database.