About

Data

The pan-genome of Burkholderia pseudomallei in this database consists of 48 complete B. pseudomallei genome that is available during the initial database development in October 2016. Due to increasing number of completed genomes of this pathogenic bacteria, we have updated the information of corresponding orthologous groups (OGs) for the total 81 genomes of B. pseudomallei complete genome up to September 2017.

In pan-genome, every gene is grouped into OG. An OG consists of orthologous genes that believe to play similar function. The OG can be assigned as (i) core gene: exist in all strains OR (ii) accessory gene: exist in some of the strain(s). When an OG has single record of gene (gene that only exist in one strain), it is denoted as singleton.

In Pan-Bp database, transcriptome data is used to describe the expression of genes in different conditions at different time. There are two transcriptome data that have been used in this database:

1. Micro-array data by Ooi et al. (2013). The genes expression in a total of 80 conditions were describe qualitatively (expressed or not expressed. Further information about the data can be found in PATRIC database (Wattam et al. 2017).
2. RNA-Seq data by in-house study (D286, H10, PMC2000, and R15). B. pseudomallei is cultured in four conditions: brain-heart infusion broth (BHIB), sodium chloride (NaCl), minimal medium (M9) and soil (soil).

Basic search function

Basic search function can be performed in three ways:

1. Gene ID
Examples: BPSL0001, BPSS0001, D286.1_0001, H10.1_0001, PMC2000.1_0001, R15.1_0001,..


2. Keywords
Examples: ABC transporter, kinase, secretion,..


3. Orthologous group
Examples: OGv1.00001, OGv2.00001,..

All search queries will return result in table that can lead user to another page of more details of particular gene. Query must be three or more characters.

Sequence search function

BLAST search is integrated to search against provided biological databases:
(a) Public databases: non-redundant (nucleotide and protein), SWISS-PROT, Protein Data Bank (PDB)
(b) B. pseudomallei database: genome and proteome of both B. pseudomallei pan-genome dataset

References

1. Blom, J., Albaum, S.P., Doppmeier, D., Puhler, A., Vorholter, F.-J., Zakrzewski, M. & Goesmann, A. 2009. EDGAR: A software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 10(1): 154.
2. Ooi, W.F., Ong, C., Nandi, T., Kreisberg, J.F., Chua, H.H., Sun, G., Chen, Y., Mueller, C., Conejero, L., Eshaghi, M., Ang, R.M.L., Liu, J., Sobral, B.W., Korbsrisate, S., Gan, Y.H., Titball, R.W., Bancroft, G.J., Valade, E. & Tan, P. 2013. The condition-dependent transcriptional landscape of Burkholderia pseudomallei. PLoS Genetics, 9(9).
3. Wattam, A.R., Davis, J.J., Assaf, R., Boisvert, S., Brettin, T., Bun, C., Conrad, N., Dietrich, E.M., Disz, T., Gabbard, J.L., Gerdes, S., Henry, C.S., Kenyon, R.W., Machi, D., Mao, C., Nordberg, E.K., Olsen, G.J., Murphy-Olson, D.E., Olson, R., Overbeek, R., Parrello, B., Pusch, G.D., Shukla, M., Vonstein, V., Warren, A., Xia, F., Yoo, H. & Stevens, R.L. 2017. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Research, 45(D1): D535-D542.