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Volumn 12, Issue , 2011, Pages

BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BLAST RING IMAGE GENERATOR; COMPUTER PROGRAM; CONTROLLED STUDY; ESCHERICHIA COLI; GENE MAPPING; GENE SEQUENCE; GENE TECHNOLOGY; GENOMICS; IMAGE ANALYSIS; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROKARYOTE; SALMONELLA; SEQUENCE ANALYSIS; ARCHAEAL GENOME; COMPARATIVE STUDY; COMPUTER GRAPHICS; COMPUTER INTERFACE; GENETICS; METHODOLOGY;

EID: 79961109150     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-402     Document Type: Article
Times cited : (2440)

References (45)
  • 4
    • 4644279904 scopus 로고    scopus 로고
    • Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data
    • 10.1186/gb-2004-5-5-r37, 416473, 15128451
    • Baerends RJ, Smits WK, de Jong A, Hamoen LW, Kok J, Kuipers OP. Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biol 2004, 5:R37. 10.1186/gb-2004-5-5-r37, 416473, 15128451.
    • (2004) Genome Biol , vol.5
    • Baerends, R.J.1    Smits, W.K.2    de Jong, A.3    Hamoen, L.W.4    Kok, J.5    Kuipers, O.P.6
  • 5
    • 33747891100 scopus 로고    scopus 로고
    • Combo: a whole genome comparative browser
    • 10.1093/bioinformatics/btl193, 16709588
    • Engels R, Yu T, Burge C, Mesirov JP, DeCaprio D, Galagan JE. Combo: a whole genome comparative browser. Bioinformatics 2006, 22:1782-1783. 10.1093/bioinformatics/btl193, 16709588.
    • (2006) Bioinformatics , vol.22 , pp. 1782-1783
    • Engels, R.1    Yu, T.2    Burge, C.3    Mesirov, J.P.4    DeCaprio, D.5    Galagan, J.E.6
  • 6
    • 3242891068 scopus 로고    scopus 로고
    • VISTA: computational tools for comparative genomics
    • 10.1093/nar/gkh458, 441596, 15215394
    • Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-279. 10.1093/nar/gkh458, 441596, 15215394.
    • (2004) Nucleic Acids Res , vol.32
    • Frazer, K.A.1    Pachter, L.2    Poliakov, A.3    Rubin, E.M.4    Dubchak, I.5
  • 7
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: multiple alignment of conserved genomic sequence with rearrangements
    • 10.1101/gr.2289704, 442156, 15231754
    • Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403. 10.1101/gr.2289704, 442156, 15231754.
    • (2004) Genome Res , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 8
    • 0346463207 scopus 로고    scopus 로고
    • BugView: a browser for comparing genomes
    • 10.1093/bioinformatics/btg383, 14693822
    • Leader DP. BugView: a browser for comparing genomes. Bioinformatics 2004, 20:129-130. 10.1093/bioinformatics/btg383, 14693822.
    • (2004) Bioinformatics , vol.20 , pp. 129-130
    • Leader, D.P.1
  • 9
    • 34447286021 scopus 로고    scopus 로고
    • Genomorama: genome visualization and analysis
    • 10.1186/1471-2105-8-204, 1906841, 17570856
    • Gans JD, Wolinsky M. Genomorama: genome visualization and analysis. BMC Bioinformatics 2007, 8:204. 10.1186/1471-2105-8-204, 1906841, 17570856.
    • (2007) BMC Bioinformatics , vol.8 , pp. 204
    • Gans, J.D.1    Wolinsky, M.2
  • 10
    • 1842821076 scopus 로고    scopus 로고
    • Visualization for genomics: the Microbial Genome Viewer
    • 10.1093/bioinformatics/bth159, 14988111
    • Kerkhoven R, van Enckevort FH, Boekhorst J, Molenaar D, Siezen RJ. Visualization for genomics: the Microbial Genome Viewer. Bioinformatics 2004, 20:1812-1814. 10.1093/bioinformatics/bth159, 14988111.
    • (2004) Bioinformatics , vol.20 , pp. 1812-1814
    • Kerkhoven, R.1    van Enckevort, F.H.2    Boekhorst, J.3    Molenaar, D.4    Siezen, R.J.5
  • 11
    • 62249097015 scopus 로고    scopus 로고
    • Genome Projector: zoomable genome map with multiple views
    • 10.1186/1471-2105-10-31, 2636772, 19166610
    • Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M. Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics 2009, 10:31. 10.1186/1471-2105-10-31, 2636772, 19166610.
    • (2009) BMC Bioinformatics , vol.10 , pp. 31
    • Arakawa, K.1    Tamaki, S.2    Kono, N.3    Kido, N.4    Ikegami, K.5    Ogawa, R.6    Tomita, M.7
  • 12
    • 58049208278 scopus 로고    scopus 로고
    • DNAPlotter: circular and linear interactive genome visualization
    • 10.1093/bioinformatics/btn578, 2612626,2612626, 18990721
    • Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120. 10.1093/bioinformatics/btn578, 2612626,2612626, 18990721.
    • (2009) Bioinformatics , vol.25 , pp. 119-120
    • Carver, T.1    Thomson, N.2    Bleasby, A.3    Berriman, M.4    Parkhill, J.5
  • 13
    • 48449095609 scopus 로고    scopus 로고
    • The CGView Server: a comparative genomics tool for circular genomes
    • 10.1093/nar/gkn179, 2447734, 18411202
    • Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008, 36:W181-184. 10.1093/nar/gkn179, 2447734, 18411202.
    • (2008) Nucleic Acids Res , vol.36
    • Grant, J.R.1    Stothard, P.2
  • 16
    • 14644438364 scopus 로고    scopus 로고
    • Circular genome visualization and exploration using CGView
    • 10.1093/bioinformatics/bti054, 15479716
    • Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21:537-539. 10.1093/bioinformatics/bti054, 15479716.
    • (2005) Bioinformatics , vol.21 , pp. 537-539
    • Stothard, P.1    Wishart, D.S.2
  • 17
    • 33644857839 scopus 로고    scopus 로고
    • GenomeDiagram: a python package for the visualization of large-scale genomic data
    • 10.1093/bioinformatics/btk021, 16377612
    • Pritchard L, White JA, Birch PR, Toth IK. GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 2006, 22:616-617. 10.1093/bioinformatics/btk021, 16377612.
    • (2006) Bioinformatics , vol.22 , pp. 616-617
    • Pritchard, L.1    White, J.A.2    Birch, P.R.3    Toth, I.K.4
  • 18
    • 42149162147 scopus 로고    scopus 로고
    • The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology
    • 10.1039/b717118h, 18414733
    • Hallin PF, Binnewies TT, Ussery DW. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst 2008, 4:363-371. 10.1039/b717118h, 18414733.
    • (2008) Mol Biosyst , vol.4 , pp. 363-371
    • Hallin, P.F.1    Binnewies, T.T.2    Ussery, D.W.3
  • 20
    • 0035961748 scopus 로고    scopus 로고
    • Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
    • 10.1093/dnares/8.1.11, 11258796
    • Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001, 8:11-22. 10.1093/dnares/8.1.11, 11258796.
    • (2001) DNA Res , vol.8 , pp. 11-22
    • Hayashi, T.1    Makino, K.2    Ohnishi, M.3    Kurokawa, K.4    Ishii, K.5    Yokoyama, K.6    Han, C.G.7    Ohtsubo, E.8    Nakayama, K.9    Murata, T.10
  • 21
    • 54949137701 scopus 로고    scopus 로고
    • MetaSim: a sequencing simulator for genomics and metagenomics
    • 10.1371/journal.pone.0003373, 2556396, 18841204
    • Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE 2008, 3:e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
    • (2008) PLoS ONE , vol.3
    • Richter, D.C.1    Ott, F.2    Auch, A.F.3    Schmid, R.4    Huson, D.H.5
  • 22
    • 0031955116 scopus 로고    scopus 로고
    • Consed: a graphical tool for sequence finishing
    • Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8:195-202.
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 24
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • 10.1093/bioinformatics/btp324, 2705234, 19451168
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 28
  • 31
    • 53849112279 scopus 로고    scopus 로고
    • Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5
    • 10.1128/JB.00661-08, 2566207, 18708504
    • Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J Bacteriol 2008, 190:6779-6794. 10.1128/JB.00661-08, 2566207, 18708504.
    • (2008) J Bacteriol , vol.190 , pp. 6779-6794
    • Fricke, W.F.1    Wright, M.S.2    Lindell, A.H.3    Harkins, D.M.4    Baker-Austin, C.5    Ravel, J.6    Stepanauskas, R.7
  • 33
    • 33645827531 scopus 로고    scopus 로고
    • Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach
    • 10.1073/pnas.0600938103, 1424661, 16585510
    • Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P, et al. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci USA 2006, 103:5977-5982. 10.1073/pnas.0600938103, 1424661, 16585510.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5977-5982
    • Chen, S.L.1    Hung, C.S.2    Xu, J.3    Reigstad, C.S.4    Magrini, V.5    Sabo, A.6    Blasiar, D.7    Bieri, T.8    Meyer, R.R.9    Ozersky, P.10
  • 34
    • 53549102749 scopus 로고    scopus 로고
    • Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
    • 10.1101/gr.077404.108, 2556274, 18583645
    • Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M, et al. Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res 2008, 18:1624-1637. 10.1101/gr.077404.108, 2556274, 18583645.
    • (2008) Genome Res , vol.18 , pp. 1624-1637
    • Thomson, N.R.1    Clayton, D.J.2    Windhorst, D.3    Vernikos, G.4    Davidson, S.5    Churcher, C.6    Quail, M.A.7    Stevens, M.8    Jones, M.A.9    Watson, M.10
  • 35
    • 15044363888 scopus 로고    scopus 로고
    • The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen
    • 10.1093/nar/gki297, 1069006, 15781495
    • Chiu CH, Tang P, Chu C, Hu S, Bao Q, Yu J, Chou YY, Wang HS, Lee YS. The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res 2005, 33:1690-1698. 10.1093/nar/gki297, 1069006, 15781495.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1690-1698
    • Chiu, C.H.1    Tang, P.2    Chu, C.3    Hu, S.4    Bao, Q.5    Yu, J.6    Chou, Y.Y.7    Wang, H.S.8    Lee, Y.S.9
  • 38
    • 9644254192 scopus 로고    scopus 로고
    • Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid
    • 10.1038/ng1470, 15531882
    • McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet 2004, 36:1268-1274. 10.1038/ng1470, 15531882.
    • (2004) Nat Genet , vol.36 , pp. 1268-1274
    • McClelland, M.1    Sanderson, K.E.2    Clifton, S.W.3    Latreille, P.4    Porwollik, S.5    Sabo, A.6    Meyer, R.7    Bieri, T.8    Ozersky, P.9    McLellan, M.10
  • 40
    • 84887212405 scopus 로고    scopus 로고
    • Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi
    • 10.1371/journal.pone.0004510, 2640428, 19229335
    • Liu WQ, Feng Y, Wang Y, Zou QH, Chen F, Guo JT, Peng YH, Jin Y, Li YG, Hu SN, et al. Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi. PLoS One 2009, 4:e4510. 10.1371/journal.pone.0004510, 2640428, 19229335.
    • (2009) PLoS One , vol.4
    • Liu, W.Q.1    Feng, Y.2    Wang, Y.3    Zou, Q.H.4    Chen, F.5    Guo, J.T.6    Peng, Y.H.7    Jin, Y.8    Li, Y.G.9    Hu, S.N.10
  • 41
    • 69049102103 scopus 로고    scopus 로고
    • Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence
    • 10.1128/IAI.00198-09, 2738036, 19564389
    • Kulasekara BR, Jacobs M, Zhou Y, Wu Z, Sims E, Saenphimmachak C, Rohmer L, Ritchie JM, Radey M, McKevitt M, et al. Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence. Infect Immun 2009, 77:3713-3721. 10.1128/IAI.00198-09, 2738036, 19564389.
    • (2009) Infect Immun , vol.77 , pp. 3713-3721
    • Kulasekara, B.R.1    Jacobs, M.2    Zhou, Y.3    Wu, Z.4    Sims, E.5    Saenphimmachak, C.6    Rohmer, L.7    Ritchie, J.M.8    Radey, M.9    McKevitt, M.10
  • 42
    • 70449568272 scopus 로고    scopus 로고
    • Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli
    • 10.1073/pnas.0903585106, 2764950, 19815525
    • Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci USA 2009, 106:17939-17944. 10.1073/pnas.0903585106, 2764950, 19815525.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 17939-17944
    • Ogura, Y.1    Ooka, T.2    Iguchi, A.3    Toh, H.4    Asadulghani, M.5    Oshima, K.6    Kodama, T.7    Abe, H.8    Nakayama, K.9    Kurokawa, K.10
  • 43
    • 58149498183 scopus 로고    scopus 로고
    • Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69
    • 10.1128/JB.01238-08, 2612414, 18952797
    • Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P, et al. Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol 2009, 191:347-354. 10.1128/JB.01238-08, 2612414, 18952797.
    • (2009) J Bacteriol , vol.191 , pp. 347-354
    • Iguchi, A.1    Thomson, N.R.2    Ogura, Y.3    Saunders, D.4    Ooka, T.5    Henderson, I.R.6    Harris, D.7    Asadulghani, M.8    Kurokawa, K.9    Dean, P.10
  • 44
    • 77649261066 scopus 로고    scopus 로고
    • Derivation of Escherichia coli O157:H7 from its O55:H7 precursor
    • 10.1371/journal.pone.0008700, 2806823, 20090843
    • Zhou Z, Li X, Liu B, Beutin L, Xu J, Ren Y, Feng L, Lan R, Reeves PR, Wang L. Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One 2010, 5:e8700. 10.1371/journal.pone.0008700, 2806823, 20090843.
    • (2010) PLoS One , vol.5
    • Zhou, Z.1    Li, X.2    Liu, B.3    Beutin, L.4    Xu, J.5    Ren, Y.6    Feng, L.7    Lan, R.8    Reeves, P.R.9    Wang, L.10


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