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xBASE, a collection of online databases for bacterial comparative genomics
Division of Immunity and Infection, University of Birmingham Birmingham, UK
*To whom correspondence should be addressed. Tel: +44 121 414 7163; Fax: +44 121 414 3454; Email: m.pallen{at}bham.ac.uk
Received September 15, 2005. Revised October 27, 2005. Accepted October 27, 2005.
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.
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