xBASE, a collection of online databases for bacterial comparative genomics

Abstract

The schema of the previously described Escherischia coli database coliBASE has been applied to a number of other bacterial taxa, under the collective name xBASE. The new databases include CampyDB for Campylobacter, Helicobacter and Wolinella; PseudoDB for pseudomonads; ClostriDB for clostridia; RhizoDB for Rhizobium and Sinorhizobium; and MycoDB, for Mycobacterium, Streptomyces and related organisms. The databases provide user friendly access to annotation and genome comparisons through a web-based graphical interface. Newly developed features include whole genome displays, 'painting' of genes according to properties such as GC content, a pattern search system to identify conserved motifs and batch BLAST searching of every protein encoded by a region. Examples of how the databases have been, and continue to be, used to generate hypotheses for subsequent laboratory investigation are presented. xBASE is available online at http://xbase.bham.ac.uk.

Figure 1

Whole genome displays generated by xBASE. (a) The genome of Mycobacterium tuberculosis CDC1551 (8), coloured according to the presence (red) or absence (blue) of orthologues in Mycobacterium bovis AF2122/97 (9). This display illustrates the regions of the M.tuberculosis backbone that have been deleted during the evolution of M.bovis. (b) The genome of Pseudomonas aeruginosa PAO1 (10), coloured by AT skew (A−T/A+T) at synonymous third codon positions. This colour scheme reflects an asymmetric mutation bias during chromosomal replication. The ‘switch’ from leading to lagging strand at the origin and terminus of replication can be seen. They are not directly opposite due to a large 2.2 Mb inversion that spans the replication origin of the P.aeruginosa genome.

Figure 2

Use of the ‘gene painting’ facility of xBASE to highlight potential type-III secretion effectors that are passenger genes within an E.coli O157:H7 specific prophage. (a) Illustrates the boundary of the phage, as determined by comparison with the E.coli K12 MG1655 genome. (b) Highlights four large genes within the prophage that have a low GC content (blue) and represent putative passenger genes. Homology searches indicate that these genes are potential type-III effectors.