메뉴 건너뛰기




Volumn 43, Issue D1, 2015, Pages D48-D53

Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; INTEGRASE; MESSENGER RNA; TRANSFER RNA; BACTERIAL RNA; TMRNA;

EID: 84946078483     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1072     Document Type: Article
Times cited : (94)

References (30)
  • 4
    • 80052333445 scopus 로고    scopus 로고
    • The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation
    • Guglielmini, J., Quintais, L., Garcillan-Barcia, M. P., de la Cruz, F. and Rocha, E. P. (2011) The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet., 7, e1002222.
    • (2011) PLoS Genet. , vol.7 , pp. e1002222
    • Guglielmini, J.1    Quintais, L.2    Garcillan-Barcia, M.P.3    De La Cruz, F.4    Rocha, E.P.5
  • 5
    • 0037030684 scopus 로고    scopus 로고
    • Filamentous phage integration requires the host recombinases XerC and XerD
    • Huber, K. E. and Waldor, M. K. (2002) Filamentous phage integration requires the host recombinases XerC and XerD. Nature, 417, 656-659.
    • (2002) Nature , vol.417 , pp. 656-659
    • Huber, K.E.1    Waldor, M.K.2
  • 6
    • 0025005169 scopus 로고
    • Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates
    • Hacker, J., Bender, L., Ott, M., Wingender, J., Lund, B., Marre, R. and Goebel, W. (1990) Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb. Pathog., 8, 213-225.
    • (1990) Microb. Pathog. , vol.8 , pp. 213-225
    • Hacker, J.1    Bender, L.2    Ott, M.3    Wingender, J.4    Lund, B.5    Marre, R.6    Goebel, W.7
  • 7
    • 0025079241 scopus 로고
    • A bacterial virulence determinant encoded by lysogenic coliphage lambda
    • Barondess, J. J. and Beckwith, J. (1990) A bacterial virulence determinant encoded by lysogenic coliphage lambda. Nature, 346, 871-874.
    • (1990) Nature , vol.346 , pp. 871-874
    • Barondess, J.J.1    Beckwith, J.2
  • 8
    • 2442449227 scopus 로고    scopus 로고
    • Genomic islands in pathogenic and environmental microorganisms
    • Dobrindt, U., Hochhut, B., Hentschel, U. and Hacker, J. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol., 2, 414-424.
    • (2004) Nat. Rev. Microbiol. , vol.2 , pp. 414-424
    • Dobrindt, U.1    Hochhut, B.2    Hentschel, U.3    Hacker, J.4
  • 9
    • 0024967060 scopus 로고
    • Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements
    • Reiter, W. D., Palm, P. and Yeats, S. (1989) Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res., 17, 1907-1914.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 1907-1914
    • Reiter, W.D.1    Palm, P.2    Yeats, S.3
  • 10
    • 0037082414 scopus 로고    scopus 로고
    • Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: Sublocation preference of integrase subfamilies
    • Williams, K. P. (2002) Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res., 30, 866-875.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 866-875
    • Williams, K.P.1
  • 11
    • 0347756648 scopus 로고    scopus 로고
    • Islander: A database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
    • Mantri, Y. and Williams, K. P. (2004) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res., 32, D55-D58.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D55-D58
    • Mantri, Y.1    Williams, K.P.2
  • 12
    • 60349117754 scopus 로고    scopus 로고
    • Genomic islands are dynamic, ancient integrative elements in bacterial evolution
    • Boyd, E. F., Almagro-Moreno, S. and Parent, M. A. (2009) Genomic islands are dynamic, ancient integrative elements in bacterial evolution. Trends Microbiol., 17, 47-53.
    • (2009) Trends Microbiol. , vol.17 , pp. 47-53
    • Boyd, E.F.1    Almagro-Moreno, S.2    Parent, M.A.3
  • 13
    • 0347756648 scopus 로고    scopus 로고
    • Islander: A database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
    • Mantri, Y. and Williams, K. P. (2004) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res., 32, D55-D58.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D55-D58
    • Mantri, Y.1    Williams, K.P.2
  • 14
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T. M. and Eddy, S. R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 0955-0964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 0955-0964
    • Lowe, T.M.1    Eddy, S.R.2
  • 15
    • 1242297827 scopus 로고    scopus 로고
    • ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
    • Laslett, D. and Canback, B. (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res., 32, 11-16.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 11-16
    • Laslett, D.1    Canback, B.2
  • 16
    • 0036682389 scopus 로고    scopus 로고
    • BRUCE: A program for the detection of transfer-messenger RNA genes in nucleotide sequences
    • Laslett, D., Canback, B. and Andersson, S. (2002) BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Res., 30, 3449-3453.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3449-3453
    • Laslett, D.1    Canback, B.2    Andersson, S.3
  • 18
    • 0036792830 scopus 로고    scopus 로고
    • tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features
    • Marck, C. and Grosjean, H. (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189-1232.
    • (2002) RNA , vol.8 , pp. 1189-1232
    • Marck, C.1    Grosjean, H.2
  • 19
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: Interactive sequence similarity searching
    • Finn, R. D., Clements, J. and Eddy, S. R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 22
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 23
    • 84864644262 scopus 로고    scopus 로고
    • Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes
    • Van Houdt, R., Leplae, R., Lima-Mendez, G., Mergeay, M. and Toussaint, A. (2012) Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. Mobile DNA, 3, 6.
    • (2012) Mobile DNA , vol.3 , pp. 6
    • Van Houdt, R.1    Leplae, R.2    Lima-Mendez, G.3    Mergeay, M.4    Toussaint, A.5
  • 24
    • 0029955368 scopus 로고    scopus 로고
    • Integration of bacteriophage Mx8 into the Myxococcus xanthus chromosome causes a structural alteration at the C-terminal region of the IntP protein
    • Tojo, N., Sanmiya, K., Sugawara, H., Inouye, S. and Komano, T. (1996) Integration of bacteriophage Mx8 into the Myxococcus xanthus chromosome causes a structural alteration at the C-terminal region of the IntP protein. J. Bacteriol., 178, 4004-4011.
    • (1996) J. Bacteriol. , vol.178 , pp. 4004-4011
    • Tojo, N.1    Sanmiya, K.2    Sugawara, H.3    Inouye, S.4    Komano, T.5
  • 25
    • 39749091834 scopus 로고    scopus 로고
    • Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival
    • Peng, X. (2008) Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival. Microbiology, 154, 383-391.
    • (2008) Microbiology , vol.154 , pp. 383-391
    • Peng, X.1
  • 26
    • 0032574728 scopus 로고    scopus 로고
    • Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene
    • Sullivan, J. T. and Ronson, C. W. (1998) Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc. Natl. Acad. Sci. U. S. A., 95, 5145-5149.
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 5145-5149
    • Sullivan, J.T.1    Ronson, C.W.2
  • 27
    • 0037310615 scopus 로고    scopus 로고
    • Traffic at the tmRNA gene
    • Williams, K. P. (2003) Traffic at the tmRNA gene. J. Bacteriol., 185, 1059-1070.
    • (2003) J. Bacteriol. , vol.185 , pp. 1059-1070
    • Williams, K.P.1
  • 28
    • 80053366291 scopus 로고    scopus 로고
    • Interactive metagenomic visualization in a Web browser
    • Ondov, B. D., Bergman, N. H. and Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12, 385.
    • (2011) BMC Bioinformatics , vol.12 , pp. 385
    • Ondov, B.D.1    Bergman, N.H.2    Phillippy, A.M.3
  • 30
    • 33748689309 scopus 로고    scopus 로고
    • Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands
    • Vernikos, G. S. and Parkhill, J. (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics, 22, 2196-2203.
    • (2006) Bioinformatics , vol.22 , pp. 2196-2203
    • Vernikos, G.S.1    Parkhill, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.