Home LiteratureArticle Details
PMID: 14681417 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.

Nucleic acids research ·Vol. 32 ·No. Database issue ·2004-01-01 ·Pages D296-9

Chaudhuri RR, Khan AM, Pallen MJ

Abstract

We have constructed coliBASE, a database for Escherichia coli, Shigella and Salmonella comparative genomics available online at http://colibase. bham.ac.uk. Unlike other E.coli databases, which focus on the laboratory model strain K12, coliBASE is intended to reflect the full diversity of E.coli and its relatives. The database contains comparative data including whole genome alignments and lists of putative orthologous genes, together with numerous analytical tools and links to existing online resources. The data are stored in a relational database, accessible by a number of user-friendly search methods and graphical browsers. The database schema is generic and can easily be applied to other bacterial genomes. Two such databases, CampyDB (for the analysis of Campylobacter spp.) and ClostriDB (for Clostridium spp.) are also available at http://campy.bham.ac.uk and http://clostri. bham.ac.uk, respectively. An example of the power of E.coli comparative analyses such as those available through coliBASE is presented.

MeSH Terms
Computational Biology Databases, Genetic Escherichia coli/genetics,metabolism Genes, Bacterial Genome, Bacterial Genomics Information Storage and Retrieval Internet Salmonella/genetics Sequence Alignment Shigella/genetics Software User-Computer Interface
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Chaudhuri Roy R
Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
Khan Arshad M
Pallen Mark J
References (31)
31 references, click to expand
  1. The SPI-3 pathogenicity island of Salmonella enterica.
    J Bacteriol. 1999 Feb;181(3):998-1004 PMID: 9922266
  2. Primer3 on the WWW for general users and for biologist programmers.
    Methods Mol Biol. 2000;132:365-86 PMID: 10547847
  3. Improved microbial gene identification with GLIMMER.
    Nucleic Acids Res. 1999 Dec 1;27(23):4636-41 PMID: 10556321
  4. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.
    Nucleic Acids Res. 2000 Jan 1;28(1):45-8 PMID: 10592178
  5. EcoGene: a genome sequence database for Escherichia coli K-12.
    Nucleic Acids Res. 2000 Jan 1;28(1):60-4 PMID: 10592181
  6. Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence.
    Bioinformatics. 1999 Oct;15(10):860-1 PMID: 10705439
  7. Functional genomics of Escherichia coli in Japan.
    Res Microbiol. 2000 Mar;151(2):121-8 PMID: 10865957
  8. Artemis: sequence visualization and annotation.
    Bioinformatics. 2000 Oct;16(10):944-5 PMID: 11120685
  9. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.
    Nucleic Acids Res. 2001 Jan 1;29(1):72-4 PMID: 11125053
  10. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.
    Nature. 2001 Jan 25;409(6819):529-33 PMID: 11206551
  11. Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli.
    J Clin Invest. 2001 Mar;107(5):539-48 PMID: 11238553
  12. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
    DNA Res. 2001 Feb 28;8(1):11-22 PMID: 11258796
  13. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
    Nature. 2001 Oct 25;413(6858):848-52 PMID: 11677608
  14. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.
    Nature. 2001 Oct 25;413(6858):852-6 PMID: 11677609
  15. The EcoCyc Database.
    Nucleic Acids Res. 2002 Jan 1;30(1):56-8 PMID: 11752253
  16. CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
    Nucleic Acids Res. 2002 Jan 1;30(1):281-3 PMID: 11752315
  17. Fast algorithms for large-scale genome alignment and comparison.
    Nucleic Acids Res. 2002 Jun 1;30(11):2478-83 PMID: 12034836
  18. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.
    Nucleic Acids Res. 2002 Oct 15;30(20):4432-41 PMID: 12384590
  19. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.
    Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17020-4 PMID: 12471157
  20. DNA Data Bank of Japan (DDBJ) in XML.
    Nucleic Acids Res. 2003 Jan 1;31(1):13-6 PMID: 12519938
  21. The EMBL Nucleotide Sequence Database: major new developments.
    Nucleic Acids Res. 2003 Jan 1;31(1):17-22 PMID: 12519939
  22. GenBank.
    Nucleic Acids Res. 2003 Jan 1;31(1):23-7 PMID: 12519940
  23. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18.
    J Bacteriol. 2003 Apr;185(7):2330-7 PMID: 12644504
  24. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.
    Infect Immun. 2003 May;71(5):2775-86 PMID: 12704152
  25. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
    Nucleic Acids Res. 1987 Feb 11;15(3):1281-95 PMID: 3547335
  26. Colibri: a functional data base for the Escherichia coli genome.
    Microbiol Rev. 1993 Sep;57(3):623-54 PMID: 8246843
  27. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies.
    Infect Immun. 1997 Jul;65(7):2685-92 PMID: 9199437
  28. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  29. The complete genome sequence of Escherichia coli K-12.
    Science. 1997 Sep 5;277(5331):1453-62 PMID: 9278503
  30. Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC.
    Nucleic Acids Res. 1998 Jan 1;26(1):46-9 PMID: 9399797
  31. Type III protein secretion systems in bacterial pathogens of animals and plants.
    Microbiol Mol Biol Rev. 1998 Jun;62(2):379-433 PMID: 9618447
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkh031
Published
2004-01-01
Pages
D296-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC308765
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkh031 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2