메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages 281-

Context-driven discovery of gene cassettes in mobile integrons using a computational grammar

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTICS; CONTEXT SENSITIVE GRAMMARS;

EID: 70449346311     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-281     Document Type: Article
Times cited : (16)

References (40)
  • 1
    • 0033485517 scopus 로고    scopus 로고
    • Improved microbial gene identification with GLIMMER
    • 10.1093/nar/27.23.4636, 148753, 10556321
    • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27(23):4636-4641. 10.1093/nar/27.23.4636, 148753, 10556321.
    • (1999) Nucleic Acids Res , vol.27 , Issue.23 , pp. 4636-4641
    • Delcher, A.L.1    Harmon, D.2    Kasif, S.3    White, O.4    Salzberg, S.L.5
  • 3
    • 34548329975 scopus 로고    scopus 로고
    • Annotation of bacterial and archaeal genomes: improving accuracy and consistency
    • 10.1021/cr068308h, 17658903
    • Overbeek R, Bartels D, Vonstein V, Meyer F. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev 2007, 107(8):3431-3447. 10.1021/cr068308h, 17658903.
    • (2007) Chem Rev , vol.107 , Issue.8 , pp. 3431-3447
    • Overbeek, R.1    Bartels, D.2    Vonstein, V.3    Meyer, F.4
  • 4
    • 0035408587 scopus 로고    scopus 로고
    • Genome annotation: from sequence to biology
    • 10.1038/35080529, 11433356
    • Stein L. Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2(7):493-503. 10.1038/35080529, 11433356.
    • (2001) Nat Rev Genet , vol.2 , Issue.7 , pp. 493-503
    • Stein, L.1
  • 7
    • 28844444029 scopus 로고    scopus 로고
    • Combined evidence annotation of transposable elements in genome sequences
    • 10.1371/journal.pcbi.0010022, 1185648, 16110336
    • Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 2005, 1(2):166-175. 10.1371/journal.pcbi.0010022, 1185648, 16110336.
    • (2005) PLoS Comput Biol , vol.1 , Issue.2 , pp. 166-175
    • Quesneville, H.1    Bergman, C.M.2    Andrieu, O.3    Autard, D.4    Nouaud, D.5    Ashburner, M.6    Anxolabehere, D.7
  • 13
    • 2942666034 scopus 로고    scopus 로고
    • From pieces to patterns: evolutionary engineering in bacterial pathogens
    • 10.1038/nrmicro909, 15152207
    • Baquero F. From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat Rev Microbiol 2004, 2(6):510-518. 10.1038/nrmicro909, 15152207.
    • (2004) Nat Rev Microbiol , vol.2 , Issue.6 , pp. 510-518
    • Baquero, F.1
  • 14
    • 0024805974 scopus 로고
    • A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons
    • 10.1111/j.1365-2958.1989.tb00153.x, 2560119
    • Stokes HW, Hall RM. A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 1989, 3(12):1669-1683. 10.1111/j.1365-2958.1989.tb00153.x, 2560119.
    • (1989) Mol Microbiol , vol.3 , Issue.12 , pp. 1669-1683
    • Stokes, H.W.1    Hall, R.M.2
  • 15
    • 0032775767 scopus 로고    scopus 로고
    • The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics
    • 10.1111/j.1749-6632.1999.tb08916.x, 10415511
    • Ji S. The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics. Annals of the New York Academy of Sciences 1999, 870:411. 10.1111/j.1749-6632.1999.tb08916.x, 10415511.
    • (1999) Annals of the New York Academy of Sciences , vol.870 , pp. 411
    • Ji, S.1
  • 16
    • 0037079055 scopus 로고    scopus 로고
    • The language of genes
    • 10.1038/nature01255, 12432405
    • Searls DB. The language of genes. Nature 2002, 420(6912):211-217. 10.1038/nature01255, 12432405.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 211-217
    • Searls, D.B.1
  • 17
    • 0035067938 scopus 로고    scopus 로고
    • Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences
    • 10.1093/bioinformatics/17.3.226, 11294788
    • Leung S, Mellish C, Robertson D. Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences. Bioinformatics 2001, 17(3):226-236. 10.1093/bioinformatics/17.3.226, 11294788.
    • (2001) Bioinformatics , vol.17 , Issue.3 , pp. 226-236
    • Leung, S.1    Mellish, C.2    Robertson, D.3
  • 18
    • 0034046133 scopus 로고    scopus 로고
    • The language of RNA: a formal grammar that includes pseudoknots
    • 10.1093/bioinformatics/16.4.334, 10869031
    • Rivas E, Eddy SR. The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics 2000, 16(4):334-340. 10.1093/bioinformatics/16.4.334, 10869031.
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 334-340
    • Rivas, E.1    Eddy, S.R.2
  • 19
    • 0000467078 scopus 로고    scopus 로고
    • Antibiotic resistance in gram-negative bacteria: the role of gene cassettes and integrons
    • 10.1016/S1368-7646(98)80026-5, 16904397
    • Hall RM, Collis CM. Antibiotic resistance in gram-negative bacteria: the role of gene cassettes and integrons. Drug Resist Updat 1998, 1(2):109-119. 10.1016/S1368-7646(98)80026-5, 16904397.
    • (1998) Drug Resist Updat , vol.1 , Issue.2 , pp. 109-119
    • Hall, R.M.1    Collis, C.M.2
  • 20
    • 66749102064 scopus 로고    scopus 로고
    • Gene cassettes and cassette arrays in mobile resistance integrons
    • 10.1111/j.1574-6976.2009.00175.x, 19416365
    • Partridge SR, Tsafnat G, Coiera E, Iredell JR. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 2009, 33(4):757-784. 10.1111/j.1574-6976.2009.00175.x, 19416365.
    • (2009) FEMS Microbiol Rev , vol.33 , Issue.4 , pp. 757-784
    • Partridge, S.R.1    Tsafnat, G.2    Coiera, E.3    Iredell, J.R.4
  • 22
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosym-biont DNA with Glimmer
    • 10.1093/bioinformatics/btm009, 2387122, 17237039
    • Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosym-biont DNA with Glimmer. Bioinformatics 2007, 23(6):673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.A.2    Powers, E.C.3    Salzberg, S.L.4
  • 23
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 24
    • 64549119505 scopus 로고    scopus 로고
    • INTEGRALL: a database and search engine for integrons, integrases and gene cassettes
    • 10.1093/bioinformatics/btp105, 19228805
    • Moura A, Soares M, Pereira C, ao NL, Henriques I, Correia A. INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 2009, 25(8):1096-1098. 10.1093/bioinformatics/btp105, 19228805.
    • (2009) Bioinformatics , vol.25 , Issue.8 , pp. 1096-1098
    • Moura, A.1    Soares, M.2    Pereira, C.3    ao, N.L.4    Henriques, I.5    Correia, A.6
  • 25
    • 58149183697 scopus 로고    scopus 로고
    • ARDB-Antibiotic Resistance Genes Database
    • 10.1093/nar/gkn656, 2686595, 18832362
    • Liu B, Pop M. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, (37 Database):D443-D447. 10.1093/nar/gkn656, 2686595, 18832362.
    • (2009) Nucleic Acids Res , vol.Database , Issue.37
    • Liu, B.1    Pop, M.2
  • 27
    • 0037350819 scopus 로고    scopus 로고
    • Comparative analysis of super-integrons: engineering extensive genetic diversity in the Vibrionaceae
    • 10.1101/gr.617103, 430272, 12618374
    • Rowe-Magnus DA, Guerout AM, Biskri L, Bouige P, Mazel D. Comparative analysis of super-integrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res 2003, 13(3):428-442. 10.1101/gr.617103, 430272, 12618374.
    • (2003) Genome Res , vol.13 , Issue.3 , pp. 428-442
    • Rowe-Magnus, D.A.1    Guerout, A.M.2    Biskri, L.3    Bouige, P.4    Mazel, D.5
  • 29
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • 10.1073/pnas.85.8.2444, 280013, 3162770
    • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85(8):2444-2448. 10.1073/pnas.85.8.2444, 280013, 3162770.
    • (1988) Proc Natl Acad Sci USA , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 31
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: multiple alignment of conserved genomic sequence with rearrangements
    • 10.1101/gr.2289704, 442156, 15231754
    • Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14(7):1394-1403. 10.1101/gr.2289704, 442156, 15231754.
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1394-1403
    • Darling, A.C.E.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 32
    • 58149528971 scopus 로고    scopus 로고
    • MetaMine-a tool to detect and analyse gene patterns in their environmental context
    • 10.1186/1471-2105-9-459, 2615450, 18957118
    • Bohnebeck U, Lombardot T, Kottmann R, Glöckner FO. MetaMine-a tool to detect and analyse gene patterns in their environmental context. BMC Bioinformatics 2008, 9:459. 10.1186/1471-2105-9-459, 2615450, 18957118.
    • (2008) BMC Bioinformatics , vol.9 , pp. 459
    • Bohnebeck, U.1    Lombardot, T.2    Kottmann, R.3    Glöckner, F.O.4
  • 33
    • 0000923503 scopus 로고
    • Asymptotic theory of certain goodness of fit criteria based on stochastic processes
    • Anderson T, Darling D. Asymptotic theory of certain goodness of fit criteria based on stochastic processes. Ann Math Statist 1952, 23(2).
    • (1952) Ann Math Statist , vol.23 , Issue.2
    • Anderson, T.1    Darling, D.2
  • 34
    • 0027462796 scopus 로고
    • The 3' conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants
    • 187754, 8494372
    • Paulsen IT, Littlejohn TG, Rådström P, Sundstrm L, Sköld O, Swedberg G, Skurray RA. The 3' conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants. Antimicrob Agents Chemother 1993, 37(4):761-768. 187754, 8494372.
    • (1993) Antimicrob Agents Chemother , vol.37 , Issue.4 , pp. 761-768
    • Paulsen, I.T.1    Littlejohn, T.G.2    Rådström, P.3    Sundstrm, L.4    Sköld, O.5    Swedberg, G.6    Skurray, R.A.7
  • 35
    • 33746903154 scopus 로고    scopus 로고
    • New integron-associated gene cassette encoding a trimethoprim-resistant DfrB-type dihydrofolate reductase
    • 10.1128/AAC.00449-06, 1538648, 16870788
    • Levings RS, Lightfoot D, Elbourne LDH, Djordjevic SP, Hall RM. New integron-associated gene cassette encoding a trimethoprim-resistant DfrB-type dihydrofolate reductase. Antimicrob Agents Chemother 2006, 50(8):2863-2865. 10.1128/AAC.00449-06, 1538648, 16870788.
    • (2006) Antimicrob Agents Chemother , vol.50 , Issue.8 , pp. 2863-2865
    • Levings, R.S.1    Lightfoot, D.2    Elbourne, L.D.H.3    Djordjevic, S.P.4    Hall, R.M.5
  • 36
    • 3343019470 scopus 로고
    • Measuring nominal scale agreement among many raters
    • Fleiss J. Measuring nominal scale agreement among many raters. Psychological Bulletin 1971, 76(5):378-382.
    • (1971) Psychological Bulletin , vol.76 , Issue.5 , pp. 378-382
    • Fleiss, J.1
  • 37
    • 0017360990 scopus 로고
    • The measurement of observer agreement for categorical data
    • 10.2307/2529310, 843571
    • Landis J, Koch G. The measurement of observer agreement for categorical data. Biometrics 1977, 33:159-174. 10.2307/2529310, 843571.
    • (1977) Biometrics , vol.33 , pp. 159-174
    • Landis, J.1    Koch, G.2
  • 40
    • 0030698334 scopus 로고    scopus 로고
    • Structure and function of 59-base element recombination sites associated with mobile gene cassettes
    • 10.1046/j.1365-2958.1997.6091980.x, 9427403
    • Stokes HW, O'Gorman DB, Recchia GD, Parsekhian M, Hall RM. Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol Microbiol 1997, 26(4):731-745. 10.1046/j.1365-2958.1997.6091980.x, 9427403.
    • (1997) Mol Microbiol , vol.26 , Issue.4 , pp. 731-745
    • Stokes, H.W.1    O'Gorman, D.B.2    Recchia, G.D.3    Parsekhian, M.4    Hall, R.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.