coliBASE

Contact:
Prof Mark Pallen
Bacterial Pathogenesis & Genomics Unit
Division of Immunity & Infection
The School of Medicine
The University of Birmingham
Vincent Drive
Edgbaston, Birmingham
B15 2TT, United Kingdom

Email: informatics-crn-enquiries[at]cs.bham.ac.uk
Website: http://www.infection.bham.ac.uk/BPAG/pallengroup.html

Escherichia coli K-12 is a ubiquitous model organism for genetics and molecular biology. Related E. coli strains are clinically important human pathogens. To better understand the relationship between the pathogenic and non-pathogenic strains, and the wider processes of bacterial genome evolution, we have constructed coliBASE, a database for comparative genomics of E. coli and related organisms such as Salmonella. A series of similar databases focusing on other bacterial taxa are available via xBASE - a collection of databases for bacterial comparative genomics.

coliBASE has been designed with ease of use as a priority. Complete genomes can be visualised; or regions of interest can be targeted by gene names, annotation text, genomic coordinates or sequence homology. The regions can be visualised and the annotation examined, and equivalent regions from different genomes can be compared. Genes in the various displays can be “painted” according to physical properties, or to illustrate the presence or absence of orthologues of the gene within the other genomes in CampyDB.

Additional tools include the applet version of Artemis, a facility for PCR primer design using primer3, and a pattern search to enable the identification of DNA motifs such as potential transcription factor binding sites. Extensive cross-links to other online resources are available, allowing the database to be used as a “portal” to easily locate required information.