xBASE, a collection of online databases for bacterial comparative genomics.
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.
Chaudhuri
Roy R
RR
Division of Immunity and Infection, University of Birmingham, Birmingham, UK.
Pallen
Mark J
MJ
D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D018511:Systems Integration; D014584:User-Computer Interface