Strain-Specific Summaries and Analyses
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Burkholderia Genome Projects - A summary of complete and in-progress sequencing projects.
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The Burkholderia Genome Database facilitates the easy comparison of multiple genome annotations arising from annotation or sequence-based searches, and couples this with improved methods for ortholog identification and contextual visualization.
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 (learn more).
November 14, 2013
Added data for near-saturation transposon mutant library (Burkholderia thailandensis E264) added based on study by Gallagher et. al. (2013). This data can be used to get a list of putative essential genes in Burkholderia thailandensis E264 based on genes that do not have transposon insertions. A list of Burkholderia thailandensis E264 genes that do NOT have transposon insertions can be found here.
A list of Burkholderia thailandensis E264 genes that have transposon insertions can be found here.
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.(More Details)