메뉴 건너뛰기




Volumn 27, Issue 1, 2018, Pages 135-145

Clustal Omega for making accurate alignments of many protein sequences

Author keywords

benchmarking; clustal omega; multiple sequence alignment; protein structure

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; MEASUREMENT ACCURACY; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SOFTWARE; CHEMISTRY; GENETICS; PROCEDURES; SEQUENCE ANALYSIS;

EID: 85032724599     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.3290     Document Type: Article
Times cited : (1230)

References (23)
  • 2
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 3
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 4
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (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
  • 5
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Kazuharu M, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Kazuharu, M.2    Kuma, K.3    Miyata, T.4
  • 6
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for multiple sequence alignments
    • Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for multiple sequence alignments. J Mol Biol 302:205–217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 7
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 8
    • 0026605537 scopus 로고
    • CLUSTAL V: improved software for multiple sequence alignment
    • Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8:189–191.
    • (1992) Comput Appl Biosci , vol.8 , pp. 189-191
    • Higgins, D.G.1    Bleasby, A.J.2    Fuchs, R.3
  • 9
    • 0141666829 scopus 로고
    • Evolution of 5S RNA and the non-randomness of base replacement
    • Sankoff D, Morel C, Cedergen RJ (1973) Evolution of 5S RNA and the non-randomness of base replacement. Nature 245:232–234.
    • (1973) Nature , vol.245 , pp. 232-234
    • Sankoff, D.1    Morel, C.2    Cedergen, R.J.3
  • 10
    • 77952039847 scopus 로고    scopus 로고
    • Sequence embedding for fast construction of guide trees for multiple sequence alignment
    • Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG (2010) Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 5:21.
    • (2010) Algorithms Mol Biol , vol.5 , pp. 21
    • Blackshields, G.1    Sievers, F.2    Shi, W.3    Wilm, A.4    Higgins, D.G.5
  • 11
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951–960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 12
    • 85019710385 scopus 로고    scopus 로고
    • Protein multiple sequence alignment benchmarking through secondary structure prediction
    • Le Q, Sievers F, Higgins DG (2017) Protein multiple sequence alignment benchmarking through secondary structure prediction. Bioinformatics 33:1331–1337.
    • (2017) Bioinformatics , vol.33 , pp. 1331-1337
    • Le, Q.1    Sievers, F.2    Higgins, D.G.3
  • 13
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27:2682–2690.
    • (1999) Nucleic Acids Res , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 14
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
    • Thompson JD, Koehl P, Ripp R, Poch O (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 61:127–136.
    • (2005) Proteins , vol.61 , pp. 127-136
    • Thompson, J.D.1    Koehl, P.2    Ripp, R.3    Poch, O.4
  • 15
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: a database of protein structure alignments for homologous families
    • Mizuguchi K, Deane CM, Blundell TL, Overington JP (1998) HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 7:2469–2471.
    • (1998) Protein Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 17
    • 84962142395 scopus 로고    scopus 로고
    • Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments
    • Fox G, Sievers F, Higgins DG (2016) Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments. Bioinformatics 32:814–820.
    • (2016) Bioinformatics , vol.32 , pp. 814-820
    • Fox, G.1    Sievers, F.2    Higgins, D.G.3
  • 19
    • 17844386108 scopus 로고    scopus 로고
    • A benchmark of multiple sequence alignment programs upon structural RNAs
    • Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33:2433–2439.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2433-2439
    • Gardner, P.P.1    Wilm, A.2    Washietl, S.3
  • 20
    • 84904601218 scopus 로고    scopus 로고
    • Simple chained guide trees give high-quality protein multiple sequence alignments
    • Boyce K, Sievers F, Higgins DG (2014) Simple chained guide trees give high-quality protein multiple sequence alignments. Proc Natl Acad Sci USA 111:10556–10561.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 10556-10561
    • Boyce, K.1    Sievers, F.2    Higgins, D.G.3
  • 21
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2–approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490.
    • (2010) PLoS One , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 22
    • 84908085080 scopus 로고    scopus 로고
    • Systematic exploration of guide-tree topology effects for small protein alignments
    • Sievers F, Hughes GM, Higgins DG (2014) Systematic exploration of guide-tree topology effects for small protein alignments. BMC Bioinform 15:338.
    • (2014) BMC Bioinform , vol.15 , pp. 338
    • Sievers, F.1    Hughes, G.M.2    Higgins, D.G.3
  • 23
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn RD, Clements J, Eddy SR (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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.