EchoBASE: An integrated post-genomic database for Escherichia coli

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Misra, Raju V ^b   Horler, Richard S P ^b   Reindl, Wolfgang ^b   Goryanin, Igor I ^a   Thomas, Gavin H ^b  

^a GLAXOSMITHKLINE   (United Kingdom)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOINFORMATICS; CATALYSIS; CELL FUNCTION; CHEMICAL REACTION; ECHOBASE; ENZYME ACTIVITY; ESCHERICHIA COLI K 12; FACTUAL DATABASE; GENE SEQUENCE; INFORMATION PROCESSING; INTERNET; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; BIOCHEMISTRY; ESCHERICHIA COLI; GENETIC DATABASE; SEQUENCE ANALYSIS; STRAIN DIFFERENCE;

DATABASES, GENETIC; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; GENOMICS; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; ESCHERICHIA COLI K12;

EID: 13444309581     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki028     Document Type: Article

References (19)

1. Blattner,F.R., Plunkett,G., III, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
2. Perna,N.T., Plunkett,G., III, Burland,V., Mau,B., Glasner,J.D., Rose,D.J., Mayhew,G.F., Evans,P.S., Gregor,J., Kirkpatrick,H.A. et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature, 409 529-533.
3. Hayashi,T., Makino,K., Ohnishi,M., Kurokawa,K., Ishii,K., Yokoyama,K., Han,C.G., Ohtsubo,E., Nakayama,K., Murata,T. et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res., 8, 11-22.
4. Welch,R.A., Burland,V., Plunkett,G., III, Redford,P., Roesch,P., Rasko,D., Buckles,E.L., Liou,S.R., Boutin,A., Hackett,J. et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA 99, 17020-17024.
5. Hinton,J.C. (1997) The Escherichia coli genome sequence: the end of an era or the start of the FUN? Mol. Microbiol. 26, 417-422.
6. Serres,M.H., Gopal,S., Nahum,L.A., Liang,P., Gaasterland,T. and Riley,M. (2001) A functional update of the Escherichia coli K-12 genome. Genome Biol., 2, RESEARCH0035.
7. Thomas,G.H. (1999) Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence. Bioinformatics, 15, 860-861.
8. Thomas,G.H. and Bettelheim,K.A. (1998) Escherichia coli on the WWW. Lett. Appl. Microbiol., 27, 122-123.
9. Rudd,K.E. (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
10. Glasner,J.D., Liss,P., Plunkett,G., III, Darling,A., Prasad,T., Rusch,M., Byrnes,A., Gilson,M., Biehl,B., Blattner,F.R. et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res., 31, 147-151.
11. Karp,P.D., Riley,M., Saier,M., Paulsen,I.T., Collado-Vides,J., Paley,S.M., Pellegrini-Toole,A., Bonavides,C. and Gama-Castro,S. (2002) The EcoCyc Database. Nucleic Acids Res., 30, 56-58.
12. Serres,M.H., Goswami,S. and Riley,M. (2004) GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res., 32, D300-D302.
13. Chaudhuri,R.R., Khan,A.M. and Pallen,M.J. (2004) coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Res., 32, D296-D299.
14. Nielsen,H., Engelbrecht,J., Brunak,S. and von Heijne,G. (1997) A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst., 8, 581-599.
15. Juncker,A.S., Willenbrock,H., von Heijne,G., Brunak,S., Nielsen,H. and Krogh,A. (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci., 12, 1652-1662.
16. Sonnhammer,E.L., von Heijne,G. and Krogh,A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
17. Tusnady,G.E. and Simon,I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics., 17, 849-850.
18. Riley,M. and Serres,M.H. (2000) Interim report on genomics of Escherichia coli. Annu. Rev. Microbiol., 54, 341-411.
19. Edwards,J.S. and Palsson,B.O. (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA, 97, 5528-5533.