Frequently Asked Questions (Go to patient questions)

How should I cite the use of the Burkholderia Genome Database?

Please cite our Bioinformatics paper by Winsor et al. (2008) .

How do I obtain nucleotide sequences for a specific genomic region?

There are a few ways you can go about doing this.

1) If you know the exact coordinates you are interested in, go to the sequence retrieval page and scroll down to a form that is titled "Retrieve a Specific Genomic Range from the Updated Database". Enter the start and stop coordinates of the region of interest and this will return all of the genomic DNA sequence within those coordinates.

2) A flat file of all intergenic regions can be downloaded

3) Each gene card contains the nucleotide sequences for the upstream 500 bp and downstream 500 bp regions.

What is the difference between product name confidence rating and localization confidence rating? What are their classifications based on?

The product name confidence rating summarizes the degree of confidence in the function of a particular protein while the localization rating summarizes the degree of confidence in a protein’s subcellular localization. It was originally developed for the Pseudomonas aeruginosa PAO1 genome annotation as part of the early Pseudomonas Community Annotation Project (PseudoCAP)

The product name confidence rating can be summarized as follows:

Class 1: Function experimentally demonstrated in a strain of the same species.

Class 2: Function of highly similar gene experimentally demonstrated in another organism (and gene context consistent in terms of pathways it is involved in, if known).

Class 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited sequence similarity to an experimentally studied gene.

Class 4: Homologs of previously reported genes of unknown function, or no similarity to any previously reported sequences.

The localization confidence rating can be summarized as follows:

Class 1: Subcellular localization experimentally demonstrated in Pseudomonas aeruginosa.

Class 2: Subcellular localization of highly similar gene experimentally demonstrated in another organism OR to a paralog experimentally demonstrated in the same organism. BLAST expect value of 10e-10 for query within 80-120% of subject length.

Class 3: Subcellular localization computationally predicted by PSORT.

Patient Questions about Burkholderia infections

The Cystic Fibrosis Foundation has put together a list of FAQs for people interested in learning more about Burkholderia cepacia complex and how it relates to people with CF.

The BC Children's Hospital also provides a list of FAQs about the Burkholderia cepacia complex.

Please note that we are researchers involved in furthering the understanding of the biology of Burkholderia spp.. Therefore, we are not qualified to answer questions regarding treatments for Cystic Fibrosis, and/or Burkholderia infections. Any medically related questions should be referred to your personal primary care physician or other medical practitioner.

Burkholderia thailandensis grown on Ashdown's agar.
(Photo Credit: mountainamoeba on flickr).