xBASE, a collection of online databases for bacterial comparative genomics

被引:56
作者
Chaudhuri, Roy R. [1 ]
Pallen, Mark J. [1 ]
机构
[1] Univ Birmingham, Div Immun & Infect, Birmingham, W Midlands, England
基金
英国生物技术与生命科学研究理事会;
关键词
D O I
10.1093/nar/gkj140
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:D335 / D337
页数:3
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