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Volumn 30, Issue 23, 2014, Pages 3293-3301

Comparative assembly hubs: Web-accessible browsers for comparative genomics

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; SHIGELLA;

EID: 84922525196     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu534     Document Type: Article
Times cited : (17)

References (28)
  • 1
    • 77956193448 scopus 로고    scopus 로고
    • Progressivemauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling, A.E. et al. (2010) progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5, e11147.
    • (2010) PLoS One , vol.5
    • Darling, A.E.1
  • 2
    • 84865231395 scopus 로고    scopus 로고
    • Transforming clinical microbiology with bacterial genome sequencing
    • Didelot, X. et al. (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet., 13, 601-612.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 601-612
    • Didelot, X.1
  • 3
    • 12344335569 scopus 로고    scopus 로고
    • DAGchainer: A tool for mining segmental genome duplications and synteny
    • Haas, B.J. et al. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics, 20, 3643-3646.
    • (2004) Bioinformatics , vol.20 , pp. 3643-3646
    • Haas, B.J.1
  • 4
    • 31544438578 scopus 로고    scopus 로고
    • Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110
    • Hayashi, K.K. et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol., 2, 2006.0007.
    • (2006) Mol. Syst. Biol. , vol.2
    • Hayashi, K.K.1
  • 5
    • 84863527487 scopus 로고    scopus 로고
    • GenomeRing: Alignment visualization based on SuperGenome coordinates
    • Herbig, A. et al. (2012) GenomeRing: alignment visualization based on SuperGenome coordinates. Bioinformatics, 28, i7-i15.
    • (2012) Bioinformatics , vol.28 , pp. i7-i15
    • Herbig, A.1
  • 6
    • 84877940570 scopus 로고    scopus 로고
    • HAL: A hierarchical format for storing and analyzing multiple genome alignments
    • Hickey, G. et al. (2013) HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics, 29, 1341-1342.
    • (2013) Bioinformatics , vol.29 , pp. 1341-1342
    • Hickey, G.1
  • 7
    • 0019639160 scopus 로고
    • Inversions between ribosomal RNA genes of Escherichia coli
    • Hill, C.W. and Harnish, B.W. (1981) Inversions between ribosomal RNA genes of Escherichia coli. Proc. Natl Acad. Sci. USA, 78, 7069-7072.
    • (1981) Proc. Natl Acad. Sci. USA , vol.78 , pp. 7069-7072
    • Hill, C.W.1    Harnish, B.W.2
  • 8
    • 79551634894 scopus 로고    scopus 로고
    • PHAST and RPHAST: Phylogenetic analysis with space/time models
    • Hubisz, M.J. et al. (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinformatics, 12, 41-51.
    • (2011) Brief. Bioinformatics , vol.12 , pp. 41-51
    • Hubisz, M.J.1
  • 9
    • 0347755531 scopus 로고    scopus 로고
    • The UCSC Table Browser data retrieval tool
    • Karolchik, D. et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493-D496.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D493-D496
    • Karolchik, D.1
  • 10
    • 84891771466 scopus 로고    scopus 로고
    • The UCSC genome browser database: 2014 update
    • Karolchik, D. et al. (2014) The UCSC genome browser database: 2014 update. Nucleic Acids Res., 42, D764-D770.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D764-D770
    • Karolchik, D.1
  • 11
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 12
    • 84880167759 scopus 로고    scopus 로고
    • E. Coli as an all-rounder: The thin line between commensalism and pathogenicity
    • Leimbach, A. et al. (2013) E. coli as an all-rounder: the thin line between commensalism and pathogenicity. Curr. Top. Microbiol. Immunol., 358, 3-32.
    • (2013) Curr. Top. Microbiol. Immunol. , vol.358 , pp. 3-32
    • Leimbach, A.1
  • 13
    • 78149470831 scopus 로고    scopus 로고
    • Comparison of 61 sequenced Escherichia coli genomes
    • Lukjancenko, O. et al. (2010) Comparison of 61 sequenced Escherichia coli genomes. Microbial. Ecol., 60, 708-720.
    • (2010) Microbial. Ecol. , vol.60 , pp. 708-720
    • Lukjancenko, O.1
  • 14
    • 0034518158 scopus 로고    scopus 로고
    • VISTA: Visualizing global DNA sequence alignments of arbitrary length
    • Mayor, C. et al. (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16, 1046-1047.
    • (2000) Bioinformatics , vol.16 , pp. 1046-1047
    • Mayor, C.1
  • 15
    • 38849149795 scopus 로고    scopus 로고
    • 28-way vertebrate alignment and conservation track in the UCSC genome browser
    • Miller, W. et al. (2007) 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genes Dev., 17, 1797-1808.
    • (2007) Genes Dev. , vol.17 , pp. 1797-1808
    • Miller, W.1
  • 16
    • 84958551166 scopus 로고    scopus 로고
    • Building a pangenome reference for a population
    • Sharan, R. (ed.)
    • Nguyen, N. et al. (2014) Building a Pangenome Reference for a Population. In: Sharan, R. (ed.) RECOMB, pp. 207-221.
    • (2014) RECOMB , pp. 207-221
    • Nguyen, N.1
  • 17
    • 77649253051 scopus 로고    scopus 로고
    • Visualizing genomes: Techniques and challenges
    • Nielsen, C.B. et al. (2010) Visualizing genomes: techniques and challenges. Nat. Methods, 7 (3 Suppl.), S5-S15.
    • (2010) Nat. Methods , vol.7 , Issue.3 , pp. S5-S15
    • Nielsen, C.B.1
  • 18
    • 70449568272 scopus 로고    scopus 로고
    • Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic. Escherichia coli
    • Ogura, Y.Y. et al. (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic. Escherichia coli. Proc. Natl Acad. Sci. USA, 106, 17939-17944.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 17939-17944
    • Ogura, Y.Y.1
  • 19
    • 0025825737 scopus 로고
    • Genetic improvement of Escherichia coli for ethanol production: Chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II
    • Ohta, K.K. et al. (1991) Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Appl. Environ. Microbiol., 57, 893-900.
    • (1991) Appl. Environ. Microbiol. , vol.57 , pp. 893-900
    • Ohta, K.K.1
  • 20
    • 80052551536 scopus 로고    scopus 로고
    • Cactus: Algorithms for genome multiple sequence alignment
    • Paten, B. et al. (2011) Cactus: algorithms for genome multiple sequence alignment. Genome Res., 21, 1512-1528.
    • (2011) Genome Res. , vol.21 , pp. 1512-1528
    • Paten, B.1
  • 21
    • 84891814834 scopus 로고    scopus 로고
    • Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC genome browser
    • Raney, B. et al. (2013) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC genome browser. Bioinformatics, 30, 1003-1005.
    • (2013) Bioinformatics , vol.30 , pp. 1003-1005
    • Raney, B.1
  • 22
    • 75549091651 scopus 로고    scopus 로고
    • ENCODE whole-genome data in the UCSC Genome Browser
    • Rosenbloom, K.R. et al. (2010) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res., 38 (Database issue), D620-D625.
    • (2010) Nucleic Acids Res. , vol.38 , Issue.DATABASE ISSUE , pp. D620-D625
    • Rosenbloom, K.R.1
  • 23
    • 79251525497 scopus 로고    scopus 로고
    • A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation
    • Sahl, J.W.J. et al. (2011) A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation. Infect. Immun., 79, 950-960.
    • (2011) Infect. Immun. , vol.79 , pp. 950-960
    • Sahl, J.W.J.1
  • 24
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • Thorvaldsdóttir, H.H. et al. (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinformatics, 14, 178-192.
    • (2013) Brief. Bioinformatics , vol.14 , pp. 178-192
    • Thorvaldsdóttir, H.H.1
  • 25
    • 59249089471 scopus 로고    scopus 로고
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    • Touchon, M. et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet., 5, e1000344.
    • (2009) PLoS Genet. , vol.5
    • Touchon, M.1
  • 26
    • 84863467493 scopus 로고    scopus 로고
    • Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes
    • Turner, P.C.P. et al. (2012) Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes. J. Ind. Microbiol. Biotechnol., 39, 629-639.
    • (2012) J. Ind. Microbiol. Biotechnol. , vol.39 , pp. 629-639
    • Turner, P.C.P.1
  • 27
    • 65449188232 scopus 로고    scopus 로고
    • Jalview version 2-A multiple sequence alignment editor and analysis workbench
    • Waterhouse, A.M. et al. (2009) Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1
  • 28
    • 37849032744 scopus 로고    scopus 로고
    • Comparative genomics search for losses of long-established genes on the human lineage
    • Zhu, J. et al. (2007) Comparative genomics search for losses of long-established genes on the human lineage. PLoS Computat. Biol., 3, e247.
    • (2007) PLoS Computat. Biol. , vol.3
    • Zhu, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.