Burkholderia Genome Database – The Burkholderia Genome Database collaborates with an international panel of expert Burkholderia researchers to provide high quality updates to genomes annotation and make cutting edge genome analysis data available.
Submitting an annotation update for one or more genes
Please submit all annotation updates to burkholderia-mail@sfu.ca
The Burkholderia Genome Database welcomes all suggested updates to Burkholderia annotations, however we encourage you to also contact the original genome sequencing center in order to ensure the changes propagate to NCBI RefSeq.
Please include the following information when submitting an annotation update
1) The locus tag for the gene.
2) A PubMed ID or link to a paper.
3) Suggested gene and protein names.
4) The gene/protein’s function and/or biological process (if known).
5) The gene’s new genomic coordinates (if applicable).
6) Your name and institution so that we can acknowledge your contribution (optional).
Consider submitting Gene Ontology (GO) terms with your annotation update.
The database is recognized as an authoritative source for high quality genome annotations and we feel users can benefit from an ontology-rich data structure providing details of function and biological processes in a specific and hierarchical manner. By having data in this format, we can utilize a wide range of tools for the purpose of improving annotation transfer and enrichment analysis associated with omics studies being conducted in many labs.
We are interested in launching a new initiative to apply a critical and conservative approach to mapping high quality, curated gene ontology (GO) terms to the B. cenocepacia J2315 and K56-2 genome annotations.
A valid GO term submission should include:
1) A locus tag
2) A valid GO term and/or accession
3) A GO evidence code
4) The PubMed ID for the paper that the GO term and evidence code are based on.
5) If term is based on sequence similarity to a better studied gene in another strain/species, please provide a cross reference for that gene.
Submitting RNA-Seq data
The Burkholderia Genome Database is interested in hosting RNA-Seq data. If you are interested in contributin, we are currently accepting:
1) Lists of differentially-expressed genes
- Please include reference genome, locus tags, PubMed IDs, metadata (e.g. experimental conditions) and your lab’s affiliation so that we can acknowledge you
- Normalized log ratios
- Significance cutoffs should be specified
2) BAM files
- Expression data can be visualized in JBrowse (example)
- Please specify the reference genome (reads must be aligned to a reference genome at burkholderia.com), PubMed IDs, metadata (e.g. experimental conditions) and your lab’s affiliation