What's New

May 13, 2010

Fixed bug on orthologs page which was preventing mouseovers from displaying gene info.

May 3 , 2010

Important: Due to a significant power upgrade affecting the entire Burnaby campus at Simon Fraser University, including all emergency power, www.burkholderia.com will have a scheduled shutdown from Friday, May 14 until Monday May 17th, 2010. We apologize in advance for the inconvenience.

April 20, 2010

New feature for performing comparative analysis of orthologous genes. It can be used for tasks such as 1) finding orthologs present in two or more strains, 2) finding putative core genome for Burkholderia, 3) finding orthologs present in one set of strains that are absent from another set or 4) returning a list of genes from one strain that do not have orthologs in another strain.

An overview of this feature as well as instructions on how to use it is available here.

Genome summary pages now include links for downloading data and more detailed information including 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 (example).

Fixed bug in gene search that prevented non-coding genes (those without computationally predicted localizations) from being returned.

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

February 9, 2010

Fixed broken GBrowse links that were being generated from GBrowse start page and producing a "500 Internal Server Error".

February 1, 2010

3 new annotation updates.

New feature: DNA motif search tool to allow searching for DNA motifs in all strains available in this database. Results can be downloaded in both comma-separated value and tab-delimited format.

New batch download feature: Ability to download high-precision ortholog predictions from links in genome menu pages (e.g. Orthologs under "Download" tab of J2315 menu) as well as the main downloads page.

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

Fixed bug in updates log search that was preventing results from being returned.

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

January 14, 2010

7 new annotation updates.

New ortholog group classification system for Burkholderia orthologs (example view and listing for group BG005276). For more details on the method, click here.

Updated all other external genome annotations using NCBI RefSeq genome annotations available as of 2009-Dec-08.

Updated PFAM predictions based on PFAM v.22. Closest human homologs recomputed using protein sequences from Ensembl v.56.

Metabolic pathway data derived from the KEGG Metabolic Pathway Database has been integrated into the gene cards and the GBrowse view of external annotations. All pathways, including KEGG-derived pathways can be searched using the advanced Boolean search tool.

New ability to link to detailed gene pages using a GI number (e.g. http://www.burkholderia.com/getAnnotation.do?gi=107021570)

Integration of new links to IslandViewer view of analyses predicting genomic islands. IslandViewer is a computational tool that integrates two sequence composition GI prediction methods (SIGI-HMM3 and IslandPath-DIMOB4) with IslandPick, the three most accurate methods known for predicting genomic islands.

New subcellular localization predictions based on PSORTb v.3.0 (manuscript in preparation). PSORTb v.3.0 can identify sub-category localizations in bacterial organelles and, for bacteria interacting with a host, differentiate proteins that are targeted to a host cell. The new version also exhibits higher sensitivity and genome prediction coverage compared to the previous version, with an average of 15% genome coverage increase for Gram-negative species.

Incorporation of computationally-predicted operons from the Database of Prokaryotic Operons (DOOR) into gene cards (example) and GBrowse (example).

Strain names updated. Burkholderia cepacia strain AMMD changed to Burkholderia ambifaria strain AMMD (Coenye et al., 2003). Burkholderia sp. 383 changed to Burkholderia lata strain 383 (Vanlaere et al. 2009). We acknowledge Deborah Yoder-Himes (Harvard) for bringing this to our attention

Burkholderia multivorans ATCC17616 was mistakenly omitted from drop-down list on the BLAST search page. This strain has now been added.

April 22, 2009

42 new annotation updates.

Please note the recent Burkholderia Genome Database publication in Bioinformatics. When acknowledging use of the database, please cite the article by Winsor et al. (2008; PMID:18842600) and not the web site URL.

PFAM predictions for all genomes have been updated using a Reversed Position Specific Blast (v.2.2.18) search of the NCBI database of position-specific scoring matrices for sequences of known PFAM classification (based on PFAM v.22.0).

The advanced search page now has an option for limiting the size (bp) of the genes returned. For example, you can now only return genes which are greater than 500 bp.

Bugs fixed: Protein and intergenic sequence download links are now working. Combined search of Pseudomonas and Burkholderia Genome Databases has been fixed.

November 20, 2008

Genome annotation for Burkholderia cenocepacia J2315 added.

New search feature: Search using gene ontology terms.

Downloads page updated: EMBL download format added. TAB- and CSV-delimited formats updated.

Gene card pages have been updated to include the following:

If you experience any problems with this new layout, please contact us.

September 15, 2008

Search efficiency improved and maximum hit limit increased from 8,000 to 30,000.

206 new annotation updates.

Updated Ortholuge ortholog predictions.

Bug with updates log search interface fixed.

August 25, 2008

33 new annotation updates.

August 1, 2008

64 new annotation updates.

June 30, 2008

Release of the full-version Burkholderia Genome Database website!

October 1, 2007

Launch of the beta-version Burkholderia Genome Database website.