August 22, 2016
Fixed bug that caused server error when attempting to download ortholog group data.
July 19, 2016
New data release: v.7.1.0. This version includes 830 additional Burkholderia strains/isolates for a total of 1185.
The latest B. dolosa AU0158 complete genome assembly is included in this release, however we will continue to host the B. dolosa AU0158 draft assembly. Due to many requests, we have transferred the older BDAG locus tags to the new assembly as synonyms and vice versa.
Updated assemblies added for 8 genomes:
Deleted assemblies for the following genomes:
New and updated ortholog predictions for 682 Burkholderia genome assemblies having less than 100 contigs.
More user-friendly visualization of orthologs. The top studied strains now appear at the beginning of the list, followed by alphabetical sorting by species name.
New implementation of gene ontology annotation downloads in CSV and Tab-delimited formats to fix missing "GO term" field and increase processing speed.
Added COG mappings for more strains based on mappings to CDD (NCBI) database hits.
January 13, 2016
Restored an option on the advanced search page to allow retrieval of proteins with no known 3D structure (for a specific isolate). This feature was available in the previous version of our database but had been inadvertently omitted from the new site.
January 12, 2016
Broken downloads page link has been fixed.
New batch download options added.
Due to damage caused by a storm, this website and the SFU emergency power supply were down between 07:00 and 18:00 PST on Tuesday, December 8 while repairs were conducted.
Service restored after power outage on SFU campus. Power to much of SFU campus was disrupted at 21:00 PDT on Sunday, December 6 and negatively impacted campus IT services and the Pseudomonas Genome Database website for over 12 hours. Thanks for your patience during this time.
Links to details about intergenic regions have been returned to the gene details images. We have enhanced this feature to include the ability to change the amount of region displayed (e.g. look further upstream into a gene, look further downstream, etc.).
Added links to the motifs to allow searching for more occurences (e.g. search for more occurences of a TF binding site).
BlastN search results and DNA Motif search results now contain a link to show all hits (highlighted in bold boxes) in context of their surrounding genes. To do this, simply click on the "Genomic Context" link under each matching sequence.
July 31, 2015
Fixed issue with server error occurring when querying proteins by subcellular localization. Enhanced speed of subcellular localization search as well.
May 19, 2015
Fixed broken download option for Blast search results. Clicking on link to download results in CSV,Excel,PDF,ODS or RTF format was returning ERR_INVALID_RESPONSE but now gives expected result.
Added links to download raw Blast results in tab-delimited (-outfmt 6) and pairwise aligment (-outfmt 0) formats.
May 14, 2015
Fixed bug in search forms where query strain was sometimes not being reset when the input box was cleared by user.
May 13, 2015
Updated search results page to allow custom display of new and pre-existing columns. To do this go up to the "Options/Filters" box and scroll through the options in the "Columns" drop-down.
Mapped Burkholderia Genome Database locus tags to old and new NCBI locus tags. This should help alleviate some confusion generated following the recent NCBI RefSeq reannotation that wiped pre-existing locus tags.
New genome annotations added for B. cenocepacia H111.
April 15, 2015
We are pleased to announce the beta release of a new and improved Burkholderia Genome Database containing annotations, sequences and metadata for hundreds of Burkholderia genomes.
New features associated with this version include:
1) Expanded capability to view sequences and annotations for 354 complete AND draft genomes with more coming very soon!
2) Improved trackicd ng of strain/isolate metadata.
3) New and updated annotations including high quality virulence factor annotations and manually annotated GO term updates.
4) New whole-genome computational analyses including the identification of pathogen-associated genes, proteins with 3D structures, subcellular localization predictions, functional domain mappings and biological pathway predictions.
5) Integration of new genome browser (JBrowse) with features well suited for viewing your own genome annotations (e.g. alternate gene annotations, quantitative data, RNA-Seq data, variant data). Note: We are also still maintaining GBrowse for those that still prefer to use it.
April 10, 2015
866 updates to gene and product names, subcellular localizations and evidence references.
Added manually curated GO terms and virulence determinants (curated by Burkholderia Genome Database)
Added virulence factor annotations from the Virulence Factor Database (VFDB).March 6, 2015
Added virulence factor annotations obtained from the PHIDIAS Victors database.
February 7, 2013
96 updates to Burkholderia gene annotations.
Added ability to specify word size in blast searches. In order to search for short, nearly exact matches, consider dropping the word size to 6 or 7 for nucleotides or to 2 for proteins.
New data and GBrowse tracks. View manually curated operon and promoter regions in GBrowse or under "Operons/Regulons" tab of gene pages.
New ability to view RNA-Seq data in GBrowse. For example, view results from the study by Yoder-Himes et al (2010) for B. cenocepacia HI2424 in GBrowse.
You can now upload RNA-Seq data (BAM file format) to GBrowse and view it in parallel with other genomic features. For an explanation on how to do this, see this overview.
New data and search feature - Added all known 3D structures with greater than 90% similarity to Burkholderia species' proteins. Based on structure data downloaded from the RCSB Protein Data Bank. For example: View a complete list of genes encoding proteins with >90% similarity to proteins with a known 3D structure in all Burkholderia strains or in strain J2315.
When performing an advanced search, you can now filter your results to only include proteins with known 3D structures. You can further filter this list by specifying limits such as a specific subcellular localization or whether the gene is/isn't essential.
44 genes have been annotated as virulence factors. A list of can be viewed and/or downloaded by using the "Browse Virulence Factors" form on the browse genome annotations page (Example: VFs in J2315).
Updated RBBH and ortholog predictions to include the 5 new strains. CDD updated to release 3.08, TIGRFAM updated to v.13.0.
Added annotations and sequences for an additional 5 complete Burkholderia genomes.
Updated list of experimental expression data for the strain summary pages. New links to individual datasets and sample pages at NCBI GEO database.
October 12, 2012
Updated whole-genome alignments using progressive Mauve. Aligned chromosomes 1, 2 and 3 of B. cenocepacia strains AU 1054, HI2424, J2315, MC0-3 and PC184.
June 6, 2012
New data and search feature - Added all known 3D structures for Burkholderia species' proteins based on the RCSB Protein Data Bank.
When performing an advanced search, you can now filter your results to only include proteins with known 3D structures.
April 27, 2012
New regulatory motif data imported from the RegTransBase database (Genomics Division, Lawrence Berkeley National Laboratory ). Data consists of transcription factor binding sites and other regulatory interactions which have been manually curated and transferred to strains of the same species (when applicable) and may be viewed on intergenic region or gene details pages (example).
6 new annotation updates.
April 10, 2012
The site was down this morning between 9:30AM to 11:15AM PST due to an unexpected campus-wide power outage. As of 11:30AM, full service appears to have been restored, however please contact us if you experience any issues.
March 13, 2012
New analysis and search feature - View list of pathogen-associated genes for various Burkholderia strains. Based on the study "The association of virulence factors with genomic islands" (Ho Sui, Fedynak, Hsiao, Langille, and Brinkman (2009), PLoS ONE). Important note on this analysis: The list of genes defined as being pathogen-associated will change as more genomes are sequenced. This analysis will be updated at a later time in order to reflect this.
March 12, 2012
We've been experiencing some issues with site loading time and BLAST search errors since the last update on March 5th. We've taken steps to deal with the issue and are continuing to monitor the site to ensure it has been fixed. Sorry for any inconvenience experienced during this period. If you continue to experience problems, please contact us.
March 5, 2012
NEW FEATURE - Major upgrade to database schema to facilitate comparative genomics analysis of draft/incomplete Burkholderia 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.
NEW FEATURE - View secondary genomic features including inverted repeats, terminators, transposon insertion sites on detailed gene and intergenic region pages.
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...
Added evidence for 280 translationally-verified Burkholderia pseudomallei strain 844 proteins mapped to B. pseudomallei strain K96243.
Gene cards and downloadable annotations contain information on protein physiochemical properties (molecular weight, isoelectric point, mean Kyte-Doolittle hydropathicity and net charge at pH 7).
January 25, 2011
326 new annotation updates.
October 12, 2010
Fixed bug on individual gene pages that caused a "requested resource is not available" error to be returned when attempting to view the 500BP downstream sequence of each gene.
Updated BLAST search to fix issue with duplicate BLAST hits to nucleotide sequences being returned.
June 28, 2010
We experienced an exceptional hardware failure in our database server over the weekend, we moved to a backup system while we replace the failed hardware and have restored full system functional as of mid-day June 29th. We apologize for the inconvenience.
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.
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.
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.