Nucleic Acids Research, 2000, Vol. 28, No. 1 60-64
© 2000 Oxford University Press
EcoGene: a genome sequence database for Escherichia coli K-12
Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, PO Box 016129, Miami, FL 33101-6129, USA
The EcoGene database provides a set of gene and protein sequences derived from the genome sequence of Escherichia coli K-12. EcoGene is a source of re-annotated sequences for the SWISS-PROT and Colibri databases. EcoGene is used for genetic and physical map compilations in collaboration with the Coli Genetic Stock Center. The EcoGene12 release includes 4293 genes. EcoGene12 differs from the GenBank annotation of the complete genome sequence in several ways, including (i) the revision of 706 predicted or confirmed gene start sites, (ii) the correction or hypothetical reconstruction of 61 frame-shifts caused by either sequence error or mutation, (iii) the reconstruction of 14 protein sequences interrupted by the insertion of IS elements, and (iv) pre-dictions that 92 genes are partially deleted gene fragments. A literature survey identified 717 proteins whose N-terminal amino acids have been verified by sequencing. 12 446 cross-references to 6835 literature citations and abstracts are provided. EcoGene is accessible at a new website: http://bmb.med.miami. edu/EcoGene/EcoWeb . Users can search and retrieve individual EcoGene GenePages or they can download large datasets for incorporation into database management systems, facilitating various genome-scale computational and functional analyses.
* Tel: +1 350 243 6055; Fax +1 305 243 3955; Email: rudd@molbio.med.miami.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Yamazaki, R. Akashi, Y. Banno, T. Endo, H. Ezura, K. Fukami-Kobayashi, K. Inaba, T. Isa, K. Kamei, F. Kasai, et al. NBRP databases: databases of biological resources in Japan Nucleic Acids Res., November 24, 2009; (2009) gkp996v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. C. Vriezen, M. Valliere, and M. A. Riley The Evolution of Reduced Microbial Killing Gen Biol Evol, November 17, 2009; 2009(0): 400 - 408. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G.-Q. Hu, J.-T. Guo, Y.-C. Liu, and H. Zhu MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction Bioinformatics, July 15, 2009; 25(14): 1843 - 1845. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Pulvermacher, L. T. Stauffer, and G. V. Stauffer Role of the sRNA GcvB in regulation of cycA in Escherichia coli Microbiology, January 1, 2009; 155(1): 106 - 114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G.-Q. Hu, X. Zheng, H.-Q. Zhu, and Z.-S. She Prediction of translation initiation site for microbial genomes with TriTISA Bioinformatics, January 1, 2009; 25(1): 123 - 125. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Klimke, R. Agarwala, A. Badretdin, S. Chetvernin, S. Ciufo, B. Fedorov, B. Kiryutin, K. O'Neill, W. Resch, S. Resenchuk, et al. The National Center for Biotechnology Information's Protein Clusters Database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D216 - D223. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G.-Q. Hu, X. Zheng, Y.-F. Yang, P. Ortet, Z.-S. She, and H. Zhu ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D114 - D119. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Macvanin, E. I. Gonzalez de Valdivia, D. H. Ardell, and L. A. Isaksson Transient Erythromycin Resistance Phenotype Associated with Peptidyl-tRNA Drop-Off on Early UGG and GGG Codons J. Bacteriol., December 15, 2007; 189(24): 8993 - 9000. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, et al. Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Res., December 3, 2007; 35(22): 7577 - 7590. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. P. Carlson Metabolic systems cost-benefit analysis for interpreting network structure and regulation Bioinformatics, May 15, 2007; 23(10): 1258 - 1264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. L. Visick, T. M. O'Shea, A. H. Klein, K. Geszvain, and A. J. Wolfe The Sugar Phosphotransferase System of Vibrio fischeri Inhibits both Motility and Bioluminescence J. Bacteriol., March 15, 2007; 189(6): 2571 - 2574. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Delcher, K. A. Bratke, E. C. Powers, and S. L. Salzberg Identifying bacterial genes and endosymbiont DNA with Glimmer Bioinformatics, March 15, 2007; 23(6): 673 - 679. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. K. Shultzaberger, Z. Chen, K. A. Lewis, and T. D. Schneider Anatomy of Escherichia coli {sigma}70 promoters Nucleic Acids Res., February 16, 2007; 35(3): 771 - 788. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Frottin, A. Martinez, P. Peynot, S. Mitra, R. C. Holz, C. Giglione, and T. Meinnel The Proteomics of N-terminal Methionine Cleavage Mol. Cell. Proteomics, December 1, 2006; 5(12): 2336 - 2349. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Vallenet, L. Labarre, Z. Rouy, V. Barbe, S. Bocs, S. Cruveiller, A. Lajus, G. Pascal, C. Scarpelli, and C. Medigue MaGe: a microbial genome annotation system supported by synteny results Nucleic Acids Res., January 10, 2006; 34(1): 53 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Riley, T. Abe, M. B. Arnaud, M. K.B. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, et al. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 Nucleic Acids Res., January 5, 2006; 34(1): 1 - 9. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Whiteford, N. Haslam, G. Weber, A. Prugel-Bennett, J. W. Essex, P. L. Roach, M. Bradley, and C. Neylon An analysis of the feasibility of short read sequencing Nucleic Acids Res., November 7, 2005; 33(19): e171 - e171. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Tech, N. Pfeifer, B. Morgenstern, and P. Meinicke TICO: a tool for improving predictions of prokaryotic translation initiation sites Bioinformatics, September 1, 2005; 21(17): 3568 - 3569. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Wu, D. E. Culley, and W. Zhang Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism Microbiology, July 1, 2005; 151(7): 2175 - 2187. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Ezraty, B. Dahlgren, and M. P. Deutscher The RNase Z Homologue Encoded by Escherichia coli elaC Gene Is RNase BN J. Biol. Chem., April 29, 2005; 280(17): 16542 - 16545. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Nishino, T. Honda, and A. Yamaguchi Genome-Wide Analyses of Escherichia coli Gene Expression Responsive to the BaeSR Two-Component Regulatory System J. Bacteriol., March 1, 2005; 187(5): 1763 - 1772. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. V. Misra, R. S. P. Horler, W. Reindl, I. I. Goryanin, and G. H. Thomas EchoBASE: an integrated post-genomic database for Escherichia coli Nucleic Acids Res., January 1, 2005; 33(suppl_1): D329 - D333. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-W. Ma, B. Kumar, U. Ditges, F. Gunzer, J. Buer, and A.-P. Zeng An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs Nucleic Acids Res., December 16, 2004; 32(22): 6643 - 6649. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. Herring and F. R. Blattner Global Transcriptional Effects of a Suppressor tRNA and the Inactivation of the Regulator frmR J. Bacteriol., October 15, 2004; 186(20): 6714 - 6720. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. B. Waites and D. F. Talkington Mycoplasma pneumoniae and Its Role as a Human Pathogen Clin. Microbiol. Rev., October 1, 2004; 17(4): 697 - 728. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Lease, D. Smith, K. McDonough, and M. Belfort The Small Noncoding DsrA RNA Is an Acid Resistance Regulator in Escherichia coli J. Bacteriol., September 15, 2004; 186(18): 6179 - 6185. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. P. Zimmer, O. Paliy, B. Thomas, P. Gyaneshwar, and S. Kustu Genome Image Programs: Visualization and Interpretation of Escherichia coli Microarray Experiments Genetics, August 1, 2004; 167(4): 2111 - 2119. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Marino-Ramirez, J. L. Minor, N. Reading, and J. C. Hu Identification and Mapping of Self-Assembling Protein Domains Encoded by the Escherichia coli K-12 Genome by Use of {lambda} Repressor Fusions J. Bacteriol., March 1, 2004; 186(5): 1311 - 1319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Nishino and A. Yamaguchi Role of Histone-Like Protein H-NS in Multidrug Resistance of Escherichia coli J. Bacteriol., March 1, 2004; 186(5): 1423 - 1429. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Sundararaj, A. Guo, B. Habibi-Nazhad, M. Rouani, P. Stothard, M. Ellison, and D. S. Wishart The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli Nucleic Acids Res., January 1, 2004; 32(90001): D293 - 295. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. R. Chaudhuri, A. M. Khan, and M. J. Pallen coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics Nucleic Acids Res., January 1, 2004; 32(90001): D296 - 299. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Lithwick and H. Margalit Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation Genome Res., December 1, 2003; 13(12): 2665 - 2673. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Nishino, J. Yamada, H. Hirakawa, T. Hirata, and A. Yamaguchi Roles of TolC-Dependent Multidrug Transporters of Escherichia coli in Resistance to {beta}-Lactams Antimicrob. Agents Chemother., September 1, 2003; 47(9): 3030 - 3033. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bocs, S. Cruveiller, D. Vallenet, G. Nuel, and C. Medigue AMIGene: Annotation of MIcrobial Genes Nucleic Acids Res., July 1, 2003; 31(13): 3723 - 3726. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. M. Riehle, A. F. Bennett, R. E. Lenski, and A. D. Long Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature Physiol Genomics, June 24, 2003; 14(1): 47 - 58. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Nishino, Y. Inazumi, and A. Yamaguchi Global Analysis of Genes Regulated by EvgA of the Two-Component Regulatory System in Escherichia coli J. Bacteriol., April 15, 2003; 185(8): 2667 - 2672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Hershberg, S. Altuvia, and H. Margalit A survey of small RNA-encoding genes in Escherichia coli Nucleic Acids Res., April 1, 2003; 31(7): 1813 - 1820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F.-B. Guo, H.-Y. Ou, and C.-T. Zhang ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes Nucleic Acids Res., March 15, 2003; 31(6): 1780 - 1789. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Gardner, C. R. Gessner, and P. R. Gardner Regulation of the Nitric Oxide Reduction Operon (norRVW) in Escherichia coli. ROLE OF NorR AND sigma 54 IN THE NITRIC OXIDE STRESS RESPONSE J. Biol. Chem., March 14, 2003; 278(12): 10081 - 10086. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. J. Cheung, V. Badarinarayana, D. W. Selinger, D. Janse, and G. M. Church A Microarray-Based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic Stress Response of Escherichia coli Genome Res., February 1, 2003; 13(2): 206 - 215. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Tjaden, R. M. Saxena, S. Stolyar, D. R. Haynor, E. Kolker, and C. Rosenow Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays Nucleic Acids Res., September 1, 2002; 30(17): 3732 - 3738. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Walker, V. Pavlovic, and S. Kasif A comparative genomic method for computational identification of prokaryotic translation initiation sites Nucleic Acids Res., July 15, 2002; 30(14): 3181 - 3191. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Liang, B. Labedan, and M. Riley Physiological genomics of Escherichia coli protein families Physiol Genomics, April 10, 2002; 9(1): 15 - 26. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Drew, D. Sjostrand, J. Nilsson, T. Urbig, C.-n. Chin, J.-W. de Gier, and G. von Heijne Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis PNAS, February 20, 2002; (2002) 52018199. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Moszer, L. M. Jones, S. Moreira, C. Fabry, and A. Danchin SubtiList: the reference database for the Bacillus subtilis genome Nucleic Acids Res., January 1, 2002; 30(1): 62 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. K. Van Dyk, E. J. DeRose, and G. E. Gonye LuxArray, a High-Density, Genomewide Transcription Analysis of Escherichia coli Using Bioluminescent Reporter Strains J. Bacteriol., October 1, 2001; 183(19): 5496 - 5505. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Courcelle, A. Khodursky, B. Peter, P. O. Brown, and P. C. Hanawalt Comparative Gene Expression Profiles Following UV Exposure in Wild-Type and SOS-Deficient Escherichia coli Genetics, May 1, 2001; 158(1): 41 - 64. [Abstract] [Full Text]
|
|
|
|
|
|
L. A. McCue, W. Thompson, C. S. Carmack, M. P. Ryan, J. S. Liu, V. Derbyshire, and C. E. Lawrence Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes Nucleic Acids Res., February 1, 2001; 29(3): 774 - 782. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Drew, D. Sjostrand, J. Nilsson, T. Urbig, C.-n. Chin, J.-W. de Gier, and G. von Heijne Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis PNAS, March 5, 2002; 99(5): 2690 - 2695. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Liang, B. Labedan, and M. Riley Physiological genomics of Escherichia coli protein families Physiol Genomics, April 10, 2002; 9(1): 15 - 26. [Abstract] [Full Text] [PDF]
|
|