메뉴 건너뛰기




Volumn 40, Issue 22, 2012, Pages

OASIS: An automated program for global investigation of bacterial and archaeal insertion sequences

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL RNA; BACTERIAL RNA; RIBOSOME RNA;

EID: 84871192427     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks778     Document Type: Article
Times cited : (34)

References (35)
  • 1
    • 85158048416 scopus 로고    scopus 로고
    • Insertion sequences revisited. Mobile DNA II
    • Craig, N. L., Craigie, R., Gellert, M. and Lambowitz, A. M. (eds Washington D. C.
    • Chandler, M. (2002) Insertion sequences revisited. Mobile DNA II. In: Craig, N. L., Craigie, R., Gellert, M. and Lambowitz, A. M. (eds), Mobile DNA II. American Society for Microbiology, Washington D. C., pp. 305-366.
    • (2002) Mobile DNA II. American Society for Microbiology , pp. 305-366
    • Chandler, M.1
  • 2
    • 41049093450 scopus 로고    scopus 로고
    • Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea
    • Zhou, F. and Olman, V. (2008) Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea. BMC Genomics, 9, 36.
    • (2008) BMC Genomics , vol.9 , pp. 36
    • Zhou, F.1    Olman, V.2
  • 3
    • 77955658052 scopus 로고    scopus 로고
    • Promiscuous DNA: Horizontal transfer of transposable elements and why it matters for eukaryotic evolution
    • Schaack, S., Gilbert, C. and Feschotte, C. (2010) Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol. Evol., 25, 537-546.
    • (2010) Trends Ecol. Evol , vol.25 , pp. 537-546
    • Schaack, S.1    Gilbert, C.2    Feschotte, C.3
  • 4
    • 70349690200 scopus 로고    scopus 로고
    • Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation
    • Chou, H.-H., Berthet, J. and Marx, C. J. (2009) Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genet., 5, e1000652.
    • (2009) PLoS Genet , vol.5
    • Chou, H.-H.1    Berthet, J.2    Marx, C.J.3
  • 5
    • 0033786720 scopus 로고    scopus 로고
    • Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements
    • Schneider, D., Duperchy, E. and Coursange, E. (2000) Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements. Genetics, 156, 477-488.
    • (2000) Genetics , vol.156 , pp. 477-488
    • Schneider, D.1    Duperchy, E.2    Coursange, E.3
  • 6
    • 84861135633 scopus 로고    scopus 로고
    • Optimization of gene expression through divergent mutational paths
    • Chou, H.-H. and Marx, C. J. (2012) Optimization of gene expression through divergent mutational paths. Cell Rep., 1, 133-140.
    • (2012) Cell Rep , vol.1 , pp. 133-140
    • Chou, H.-H.1    Marx, C.J.2
  • 7
    • 84863668598 scopus 로고    scopus 로고
    • Repeated, selection-driven genome reduction of accessory genes in experimental populations
    • Lee, M.-C. and Marx, C. J. (2012) Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet., 8, e1002651.
    • (2012) PLoS Genet , vol.8
    • Lee, M.-C.1    Marx, C.J.2
  • 8
    • 0035046481 scopus 로고    scopus 로고
    • Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B
    • Cooper, V. S., Schneider, D., Blot, M. and Lenski, R. E. (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J. Bacteriol., 183, 2834-2841.
    • (2001) J. Bacteriol , vol.183 , pp. 2834-2841
    • Cooper, V.S.1    Schneider, D.2    Blot, M.3    Lenski, R.E.4
  • 11
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E. and Kim, J. F. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, 461, 1243-1247.
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1    Yu, D.S.2    Yoon, S.H.3    Jeong, H.4    Oh, T.K.5    Schneider, D.6    Lenski, R.E.7    Kim, J.F.8
  • 12
    • 79957958115 scopus 로고    scopus 로고
    • Diminishing returns epistasis among beneficial mutations decelerates adaptation
    • Chou, H.-H., Chiu, H.-C., Delaney, N. F., Segrè, D. and Marx, C. J. (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science, 332, 1190-1192.
    • (2011) Science , vol.332 , pp. 1190-1192
    • Chou, H.-H.1    Chiu, H.-C.2    Delaney, N.F.3    Segrè, D.4    Marx, C.J.5
  • 14
    • 79953119888 scopus 로고    scopus 로고
    • ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes
    • Varani, A. M., Siguier, P., Gourbeyre, E., Charneau, V. and Chandler, M. (2011) ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol., 12, R30.
    • (2011) Genome Biol , vol.12
    • Varani, A.M.1    Siguier, P.2    Gourbeyre, E.3    Charneau, V.4    Chandler, M.5
  • 15
    • 34548764905 scopus 로고    scopus 로고
    • A survey of bacterial insertion sequences using IScan
    • Wagner, A. and Lewis, C. (2007) A survey of bacterial insertion sequences using IScan. Nucleic Acids Res., 35, 5284-5293.
    • (2007) Nucleic Acids Res , vol.35 , pp. 5284-5293
    • Wagner, A.1    Lewis, C.2
  • 16
    • 54349125857 scopus 로고    scopus 로고
    • Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences
    • Wagner, A. (2008) Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Mol. Genet. Genomics, 280, 397-408.
    • (2008) Mol. Genet. Genomics , vol.280 , pp. 397-408
    • Wagner, A.1
  • 17
    • 65949106800 scopus 로고    scopus 로고
    • Methylobacterium genome sequences: A reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources
    • Vuilleumier, S., Chistoserdova, L., Lee, M.-C., Bringel, F., Lajus, A., Zhou, Y., Gourion, B., Barbe, V., Chang, J., Cruveiller, S. et al. (2009) Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PloS One, 4, e5584.
    • (2009) PloS One , vol.4
    • Vuilleumier, S.1    Chistoserdova, L.2    Lee, M.-C.3    Bringel, F.4    Lajus, A.5    Zhou, Y.6    Gourion, B.7    Barbe, V.8    Chang, J.9    Cruveiller, S.10
  • 19
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin, M., Blackshields, G. and Brown, N. (2007) Clustal W and Clustal X version 2. 0. Bioinformatics, 23, 2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.1    Blackshields, G.2    Brown, N.3
  • 20
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 21
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree of Life v2: Online annotation and display of phylogenetic trees made easy
    • Letunic, I. and Bork, P. (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res., 39, W475-W478.
    • (2011) Nucleic Acids Res , vol.39
    • Letunic, I.1    Bork, P.2
  • 22
    • 34248682119 scopus 로고    scopus 로고
    • Novel method to identify source-associated phylogenetic clustering shows that Listeria monocytogenes includes niche-adapted clonal groups with distinct ecological preferences
    • Nightingale, K. K., Lyles, K., Ayodele, M., Jalan, P., Nielsen, R. and Wiedmann, M. (2006) Novel method to identify source-associated phylogenetic clustering shows that Listeria monocytogenes includes niche-adapted clonal groups with distinct ecological preferences. J. Clin. Microbiol., 44, 3742-3751.
    • (2006) J. Clin. Microbiol , vol.44 , pp. 3742-3751
    • Nightingale, K.K.1    Lyles, K.2    Ayodele, M.3    Jalan, P.4    Nielsen, R.5    Wiedmann, M.6
  • 23
    • 0028028182 scopus 로고
    • Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
    • Stackebrandt, E. (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol., 44, 846-849.
    • (1994) Int. J. Syst. Bacteriol , vol.44 , pp. 846-849
    • Stackebrandt, E.1
  • 24
    • 0345566149 scopus 로고    scopus 로고
    • A guided tour to approximate string matching
    • Navarro, G. (2001) A guided tour to approximate string matching. ACM Comput. Surv., 33, 31-88.
    • (2001) ACM Comput. Surv , vol.33 , pp. 31-88
    • Navarro, G.1
  • 25
    • 57449109520 scopus 로고    scopus 로고
    • Transposable elements as genomic diseases
    • Wagner, A. (2009) Transposable elements as genomic diseases. Mol. BioSystems, 5, 32-35.
    • (2009) Mol. BioSystems , vol.5 , pp. 32-35
    • Wagner, A.1
  • 26
    • 34047240364 scopus 로고    scopus 로고
    • Causes of insertion sequences abundance in prokaryotic genomes
    • Touchon, M. and Rocha, E. P. C. (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol. Biol. Evol., 24, 969-981.
    • (2007) Mol. Biol. Evol , vol.24 , pp. 969-981
    • Touchon, M.1    Rocha, E.P.C.2
  • 27
    • 0034618559 scopus 로고    scopus 로고
    • Genome sequence of the endocellular bacterial symbiont of aphids: Buchnera sp
    • Sakaki, Y., Shigenobu, S., Watanabe, H., Hattori, M. and Ishikawa, H. (2000) Genome sequence of the endocellular bacterial symbiont of aphids: Buchnera sp. APS. Nature, 407, 81-86.
    • (2000) APS. Nature , vol.407 , pp. 81-86
    • Sakaki, Y.1    Shigenobu, S.2    Watanabe, H.3    Hattori, M.4    Ishikawa, H.5
  • 28
    • 0032127258 scopus 로고    scopus 로고
    • Reductive evolution of resident genomes
    • Andersson, S. G. and Kurland, C. G. (1998) Reductive evolution of resident genomes. Trends Microbiol., 6, 263-268.
    • (1998) Trends Microbiol , vol.6 , pp. 263-268
    • Andersson, S.G.1    Kurland, C.G.2
  • 29
    • 80053189514 scopus 로고    scopus 로고
    • Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus
    • Luo, H., Friedman, R., Tang, J. and Hughes, A. L. (2011) Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Mol. Biol. Evol., 28, 2751-2760.
    • (2011) Mol. Biol. Evol , vol.28 , pp. 2751-2760
    • Luo, H.1    Friedman, R.2    Tang, J.3    Hughes, A.L.4
  • 31
    • 8644224924 scopus 로고    scopus 로고
    • Genomic changes following host restriction in bacteria
    • Moran, N. and Plague, G. (2004) Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev., 14, 627-633.
    • (2004) Curr. Opin. Genet. Dev , vol.14 , pp. 627-633
    • Moran, N.1    Plague, G.2
  • 32
    • 33645221999 scopus 로고    scopus 로고
    • The nature and dynamics of bacterial genomes
    • Ochman, H. and Davalos, L. M. (2006) The nature and dynamics of bacterial genomes. Science, 311, 1730-1733.
    • (2006) Science , vol.311 , pp. 1730-1733
    • Ochman, H.1    Davalos, L.M.2
  • 33
    • 33644899969 scopus 로고    scopus 로고
    • Periodic extinctions of transposable elements in bacterial lineages: Evidence from intragenomic variation in multiple genomes
    • Wagner, A. (2006) Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol., 23, 723-733.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 723-733
    • Wagner, A.1
  • 34
    • 0026735995 scopus 로고
    • The evolution of insertion sequences within enteric bacteria
    • Lawrence, J. G., Ochman, H. and Hartl, D. L. (1992) The evolution of insertion sequences within enteric bacteria. Genetics, 131, 9-20.
    • (1992) Genetics , vol.131 , pp. 9-20
    • Lawrence, J.G.1    Ochman, H.2    Hartl, D.L.3
  • 35
    • 0034641731 scopus 로고    scopus 로고
    • Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics
    • Pupo, G. M., Lan, R. and Reeves, P. R. (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl Acad. Sci. USA, 97, 10567-10572.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 10567-10572
    • Pupo, G.M.1    Lan, R.2    Reeves, P.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.