OperonDB: A comprehensive database of predicted operons in microbial genomes

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Pertea, Mihaela ^a   Ayanbule, Kunmi ^a   Smedinghoff, Megan ^a   Salzberg, Steven L ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; BACTERIAL GENOME; COMPUTER INTERFACE; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC DATABASE; GENOME ANALYSIS; INTERNET; MATHEMATICAL COMPUTING; OPERON; OPERON DATABASE; PREDICTION; PRIORITY JOURNAL;

ALGORITHMS; DATABASES, NUCLEIC ACID; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMICS; INTERNET; OPERON; USER-COMPUTER INTERFACE;

BACTERIA (MICROORGANISMS);

EID: 58149197596     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn784     Document Type: Article

References (11)

1. Lawrence,J.G. and Roth,J.R. (1996) Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics, 143, 1843-1860.
2. Sabatti,C., Rohlin,L., Oh,M.K. and Liao,J.C. (2002) Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res., 30, 2886-2893.
3. De Hoon,M.J., Imoto,S., Kobayashi,K., Ogasawara,N. and Miyano,S. (2004) Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pac. Symp. Biocomput., 276-287.
4. Ermolaeva,M.D., White,O. and Salzberg,S.L. (2001) Prediction of operons in microbial genomes. Nucleic Acids Res., 29, 1216-1221.
5. Ermolaeva,M.D. (2005) Operon finding in bacteria. In Subramaniam, S. (ed), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, New York, pp. 2886-2891.
6. Altschul,S., Gish,W., Miller,W., Myers,E. and Lipman,D. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
7. He,X. and Goldwasser,M.H. (2005) Identifying conserved gene clusters in the presence of homology families. J. Comput. Biol., 12, 638-656.
8. Wolf,Y.I., Rogozin,I.B., Grishin,N.V. and Koonin,E.V. (2002) Genome trees and the tree of life. Trends Genet., 18, 472-479.
9. Gama-Castro,S., Jimenez-Jacinto,V., Peralta-Gil,M., Santos-Zavaleta,A., Penaloza-Spinola,M.I., Contreras-Moreira, Segura-Salazar,J., Muniz-Rascado,L., Martinez-Flores,I., Salgado,H. et al. (2008) RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res., 36, D120-D124.
10. Price,M.N., Huang,K.H., Alm,E.J. and Arkin,A.P. (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res., 33, 880-892.
11. Kingsford,C.L., Ayanbule,K. and Salzberg,S.L. (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol., 8 R22.