NEWS

November 22, 2011

A major campus-wide power outage disrupted service for several hours today. All resources now appear to be restored.

November 15, 2011

Downloadable annotation files (TAB-delimited and CSV) have new columns containing information on gene/protein length and protein physiochemical properties (molecular weight, isoelectric point, mean Kyte-Doolittle hydropathicity and net charge at pH 7).

Fixed a bug that was padding references (PMIDs) column of annotation files with a "1".

October 19, 2011

Updated ortholog predictions to include some missing P. aeruginosa LESB58 and P. putida KT2440 reciprocal best-BLAST hits.

September 26, 2011

The ability to display all genomes in GBrowse has been restored. Sorry for any inconvenience experienced during this outage.

September 23, 2011

The GBrowse viewer is currently undergoing a reconfiguration to address an ongoing server error that has developed. Unfortunately, it may be out of service during the period of September 23-26.

August 25, 2011

NEW FEATURE - The Pseudomonas Genome Database schema has undergone a significant upgrade in order to facilitate comparative genomics analysis of draft/incomplete Pseudomonas genomes

Note: Incomplete/draft genomes are often poorly annotated. Therefore, it is a good idea to supplement a text search with a BLAST or ortholog search.

Comparative genomics analysis including predicted orthologs and paralogs can now be performed for both complete and draft genomes. SNPs and small indels in draft P. aeruginosa genomes (relative to PAO1 reference sequence) can also be viewed (example).

NEW FEATURE - View secondary genomic features including inverted repeats, terminators, transposon insertion sites on detailed gene and intergenic region pages(example).

NEW FEATURE - View annotations/sequences for intergenic regions in a manner similar to our detailed gene reports. View genomic featues including regulatory motifs, inverted repeats, predicted transcription terminators, etc...

54 annotation updates.

Updated pre-computed whole-genome alignments based on the Mauve progressive alignment algorithm.

Upgraded to GBrowse 2.38. This new version contains enhanced features for viewing and downloading track data.

New protein domain predictions based on the NCBI Conserved Domains Database (CDD). This resource includes domain models from several external databases including Pfam, SMART, COG, PRK and TIGRFAM. These annotations can be viewed on individual gene pages or in GBrowse (example).

(More...)