RAC: Repository of antibiotic resistance cassettes

Database

Volumn 2011, Issue , 2011, Pages

  Tsafnat, Guy ^a   Copty, Joseph ^a   Partridge, Sally R ^b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC DATABASE; GENETICS; GRAM NEGATIVE BACTERIUM; INTERSPERSED REPEAT; METHODOLOGY; MOLECULAR GENETICS;

ANTI-BACTERIAL AGENTS; DATABASES, GENETIC; DRUG RESISTANCE, BACTERIAL; GENES, BACTERIAL; GRAM-NEGATIVE BACTERIA; INTERSPERSED REPETITIVE SEQUENCES; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84858761423     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bar054     Document Type: Article

References (23)

1. Stokes, H. W. and Gillings, M. R. (2011) Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol. Rev., 35, 790-819.
2. Partridge, S. R., Tsafnat, G., Coiera, E. et al. (2009) Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol. Rev., 33, 757-784.
3. Cambray, G., Guerout, A. M. and Mazel, D. (2010) Integrons. Annu. Rev. Genet., 44, 141-166.
4. Stokes, H. W. and Hall, R. M. (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: Integrons. Mol. Microbiol., 3, 1669-1683. (Pubitemid 20023246)
5. Gillings, M., Boucher, Y., Labbate, M. et al. (2008) The evolution of class 1 integrons the rise of antibiotic resistance. J. Bacteriol., 190 5095-5100. (Pubitemid 351991077)
6. Partridge, S. R. (2011) Analysis of antibiotic resistance regions in Gram-negative bacteria. FEMS Microbiol. Rev., 35, 820-855.
7. Hansson, K., Sundström, L., Pelletier, A. et al. (2002) IntI2 integron integrase in Tn7. J. Bacteriol., 184 1712-1721. (Pubitemid 34188223)
8. Collis, C. M., Kim, M. J., Partridge, S. R. et al. (2002) Characterization of the class 3 integron the site-specific recombination system it determines. J. Bacteriol. 184 3017-3026. (Pubitemid 34517825)
9. Wozniak, R. A., Fouts, D. E., Spagnoletti, M. et al. (2009) Comparative ICE genomics: Insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 5 e1000786.
10. Hall, R. and Partridge, S. (2003) Unambiguous numbering of antibiotic resistance genes. Antimicrob. Agents Chemother., 47, 3998; discussion 3998-3999.
11. Lee, S. H. and Jeong, S. H. (2005) Nomenclature of GES-type extended-spectrum b-lactamases. Antimicrob. Agents Chemother., 49, 2148; author reply 2148-2150.
12. White, P. A. and Rawlinson, W. D. (2001) Current status of the aadA and dfr gene cassette families. J. Antimicrob. Chemother., 47, 495-496. (Pubitemid 32303423)
13. Rowe-Magnus, D. A., Guerout, A. M., Biskri, L. et al. (2003) Comparative analysis of superintegrons: Engineering extensive genetic diversity in the Vibrionaceae. Genome Res., 13, 428-442. (Pubitemid 36395401)
14. Joss, M. J., Koenig, J. E., Labbate, M. et al. (2009) ACID: Annotation of cassette and integron data. BMC Bioinformatics, 10, 118.
15. Moura, A., Soares, M., Pereira, C. et al. (2009) INTEGRALL: A database and search engine for integrons, integrases and gene cassettes. Bioinformatics, 25, 1096-1098.
16. Liu, B. and Pop, M. (2009) ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res., 37, D443-D447.
17. Rather, P. N., Munayyer, H., Mann, P. A. et al. (1992) Genetic analysis of bacterial acetyltransferases: Identification of amino acids determining the specificities of the aminoglycoside 60-N-acetyltransferase Ib and IIa proteins. J. Bacteriol., 174, 3196-203.
18. Robicsek, A., Strahilevitz, J., Jacoby, G. A. et al. (2006) Fluoroquinolone-modifying enzyme: A new adaptation of a common aminoglycoside acetyltransferase. Nat. Med., 12, 83-88. (Pubitemid 43050081)
19. Tsafnat, G., Coiera, E., Partridge, S. R. et al. (2009) Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. BMC Bioinformatics, 10, 281.
20. Ji, S. (1999) The linguistics of DNA: Words, sentences, grammar, phonetics, and semantics. Ann. N Y Acad. Sci., 870, 411-417.
21. Schaeffer, J., Held, A. and Tsafnat, G. (2010) Computational grammars for interrogation of genomes. In: Sintchenko, V. (ed). Infectious Diseases Bioinformatics. Springer, New York, pp. 263-278.
22. Tsafnat, G., Schaeffer, J., Clayphan, A. et al. (2011) Computational inference of grammars for larger-than-gene structures from annotated gene sequences. Bioinformatics, 27, 791-796.
23. Altschul, S. F., Gish, W., Miller, W. et al. (1990) Basic local alignment search tool. J Mol Biol, 215, 403-410.