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Nucleic Acids Research 2006 34(Database Issue):D335-D337; doi:10.1093/nar/gkj140
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Nucleic Acids Research, 2006, Vol. 34, Database issue D335-D337
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

xBASE, a collection of online databases for bacterial comparative genomics

Roy R. Chaudhuri and Mark J. Pallen*

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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