메뉴 건너뛰기




Volumn 28, Issue 2, 2012, Pages 160-166

Using Sybil for interactive comparative genomics of microbes on the web

Author keywords

[No Author keywords available]

Indexed keywords

STREPTOCOCCUS PNEUMONIAE;

EID: 84856100047     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr652     Document Type: Article
Times cited : (49)

References (33)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 2
    • 79551599525 scopus 로고    scopus 로고
    • Mugsy: fast multiple alignment of closely related whole genomes
    • Angiuoli,S.V. and Salzberg,S.L. (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics, 27, 334-342.
    • (2011) Bioinformatics , vol.27 , pp. 334-342
    • Angiuoli, S.V.1    Salzberg, S.L.2
  • 3
    • 79959653780 scopus 로고    scopus 로고
    • Improving pan-genome annotation using whole genome multiple alignment
    • Angiuoli,S.V. et al. (2011a) Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinformatics, 12, 272.
    • (2011) BMC Bioinformatics , vol.12 , pp. 272
    • Angiuoli, S.V.1
  • 4
    • 80052121849 scopus 로고    scopus 로고
    • CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
    • Angiuoli,S.V. et al. (2011b) CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BC Bioinformatics, 12, 356.
    • (2011) BC Bioinformatics , vol.12 , pp. 356
    • Angiuoli, S.V.1
  • 5
    • 75549090164 scopus 로고    scopus 로고
    • The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
    • Arnaud,M.B. et al. (2010) The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res., 38, D420-D427.
    • (2010) Nucleic Acids Res. , vol.38
    • Arnaud, M.B.1
  • 6
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • Bendtsen,J.D. et al. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
    • (2004) J. Mol. Biol. , vol.340 , pp. 783-795
    • Bendtsen, J.D.1
  • 7
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette,M. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708-715.
    • (2004) Genome Res. , vol.14 , pp. 708-715
    • Blanchette, M.1
  • 8
    • 41449117976 scopus 로고    scopus 로고
    • Sybil: methods and software for multiple genome comparison and visualization
    • Crabtree,J. et al. (2007) Sybil: methods and software for multiple genome comparison and visualization. Methods Mol. Biol., 408, 93-108.
    • (2007) Methods Mol. Biol. , vol.408 , pp. 93-108
    • Crabtree, J.1
  • 9
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: multiple alignment of conserved genomic sequence with rearrangements
    • Darling,A.C. et al. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res., 14, 1394-1403.
    • (2004) Genome Res. , vol.14 , pp. 1394-1403
    • Darling, A.C.1
  • 10
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 11
    • 3242891068 scopus 로고    scopus 로고
    • VISTA: computational tools for comparative genomics
    • Frazer,K.A. et al. (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res., 32, W273-W279.
    • (2004) Nucleic Acids Res. , vol.32
    • Frazer, K.A.1
  • 12
    • 0345237922 scopus 로고    scopus 로고
    • IslandPath: aiding detection of genomic islands in prokaryotes
    • Hsiao,W. et al. (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics, 19, 418-420.
    • (2003) Bioinformatics , vol.19 , pp. 418-420
    • Hsiao, W.1
  • 13
    • 0000210258 scopus 로고
    • Nouvelles recherches sur la distribution florale
    • Jaccard,P. (1908) Nouvelles recherches sur la distribution florale. Bull. Soc. Vaudense Sci. Naturel., 44, 223-270.
    • (1908) Bull. Soc. Vaudense Sci. Naturel. , vol.44 , pp. 223-270
    • Jaccard, P.1
  • 14
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent,W.J. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996- 1006.
    • (2002) Genome Res. , vol.12 , pp. 996-1006
    • Kent, W.J.1
  • 15
    • 0025605617 scopus 로고
    • A semi-empirical method for prediction of antigenic determinants on protein antigens
    • Kolaskar,A.S. and Tongaonkar,P.C. (1990) A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett., 276, 172-174.
    • (1990) FEBS Lett. , vol.276 , pp. 172-174
    • Kolaskar, A.S.1    Tongaonkar, P.C.2
  • 16
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh,A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1
  • 17
    • 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
  • 18
    • 33751104704 scopus 로고    scopus 로고
    • Improved method for predicting linear B-cell epitopes
    • Larsen,J.E. et al. (2006) Improved method for predicting linear B-cell epitopes. Immunome Res., 2, 2.
    • (2006) Immunome Res. , vol.2 , pp. 2
    • Larsen, J.E.1
  • 19
    • 84856105194 scopus 로고    scopus 로고
    • Phobos 3.3.11. Available at
    • Mayer,C. (2006-2011) Phobos 3.3.11. Available at http://www.rub.de/spezzoo/cm/cmphobos.htm.
    • (2006)
    • Mayer, C.1
  • 20
    • 77956969931 scopus 로고    scopus 로고
    • Using the Generic Synteny Browser (GBrowse_syn)
    • Chapter 9 Unit
    • McKay,S.J. et al. (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr. Protoc. Bioinformatics, Chapter 9, Unit 9 12.
    • (2010) Curr. Protoc. Bioinformatics , vol.9 , pp. 12
    • McKay, S.J.1
  • 21
    • 50149115661 scopus 로고    scopus 로고
    • Serotype replacement and multiple resistance in Streptococcus pneumoniae after the introduction of the conjugate pneumococcal vaccine
    • Mera,R. et al. (2008) Serotype replacement and multiple resistance in Streptococcus pneumoniae after the introduction of the conjugate pneumococcal vaccine. Microb. Drug. Resist., 14, 101-107.
    • (2008) Microb. Drug. Resist. , vol.14 , pp. 101-107
    • Mera, R.1
  • 22
    • 34547844136 scopus 로고    scopus 로고
    • A Chado case study: an ontology-based modular schema for representing genome-associated biological information
    • Mungall,C.J. and Emmert,D.B. (2007) A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, i337-i346.
    • (2007) Bioinformatics , vol.23
    • Mungall, C.J.1    Emmert, D.B.2
  • 23
    • 77649253051 scopus 로고    scopus 로고
    • Visualizing genomes: techniques and challenges
    • Nielsen,C.B. et al. (2010) Visualizing genomes: techniques and challenges. Nat. Methods, 7, S5-S15.
    • (2010) Nat. Methods , vol.7
    • Nielsen, C.B.1
  • 24
    • 69949111769 scopus 로고    scopus 로고
    • Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates
    • O'Brien,K.L. et al. (2009) Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet, 374, 893-902.
    • (2009) Lancet , vol.374 , pp. 893-902
    • O'Brien, K.L.1
  • 25
    • 77954199176 scopus 로고    scopus 로고
    • Ergatis: a web interface and scalable software system for bioinformatics workflows
    • Orvis,J. et al. (2010) Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics, 26, 1488-1492.
    • (2010) Bioinformatics , vol.26 , pp. 1488-1492
    • Orvis, J.1
  • 26
    • 24144478551 scopus 로고    scopus 로고
    • SynBrowse: a synteny browser for comparative sequence analysis
    • Pan,X. et al. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics, 21, 3461-3468.
    • (2005) Bioinformatics , vol.21 , pp. 3461-3468
    • Pan, X.1
  • 27
    • 77958454595 scopus 로고    scopus 로고
    • Reverse vaccinology: developing vaccines in the era of genomics
    • Sette,A. and Rappuoli,R. (2010) Reverse vaccinology: developing vaccines in the era of genomics. Immunity, 33, 530-541.
    • (2010) Immunity , vol.33 , pp. 530-541
    • Sette, A.1    Rappuoli, R.2
  • 28
    • 61649083057 scopus 로고    scopus 로고
    • BioMart-biological queries made easy
    • Smedley,D. et al. (2009) BioMart-biological queries made easy. BMC Genomics, 10, 22.
    • (2009) BMC Genomics , vol.10 , pp. 22
    • Smedley, D.1
  • 29
    • 84856119149 scopus 로고    scopus 로고
    • RepeatMasker Open-3.0. Available at
    • Smit,A.F.A. et al. (1996) RepeatMasker Open-3.0. Available at http://www.repeatmasker.org.
    • (1996)
    • Smit, A.F.A.1
  • 30
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Perl modules for the life sciences
    • Stajich,J.E. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
    • (2002) Genome Res. , vol.12 , pp. 1611-1618
    • Stajich, J.E.1
  • 31
    • 18644378331 scopus 로고    scopus 로고
    • The generic genome browser: a building block for a model organism system database
    • Stein,L.D. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
    • (2002) Genome Res. , vol.12 , pp. 1599-1610
    • Stein, L.D.1
  • 32
    • 33748679341 scopus 로고    scopus 로고
    • SynView: a GBrowse-compatible approach to visualizing comparative genome data
    • Wang,H. et al. (2006) SynView: a GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics, 22, 2308-2309.
    • (2006) Bioinformatics , vol.22 , pp. 2308-2309
    • Wang, H.1
  • 33
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3 0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • Yu,N.Y. et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26, 1608-1615.
    • (2010) Bioinformatics , vol.26 , pp. 1608-1615
    • Yu, N.Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.