메뉴 건너뛰기




Volumn 32, Issue 5, 2004, Pages 1792-1797

MUSCLE: Multiple sequence alignment with high accuracy and high throughput

(1)  Edgar, Robert C a  

a NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BALIBASE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; HIGH THROUGHPUT SCREENING; INTERMETHOD COMPARISON; INTERNET; PREFAB; PRIORITY JOURNAL; PROTEIN DATABASE; SABMARK; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SMART; STATISTICAL ANALYSIS; COMPARATIVE STUDY; EVALUATION; METHODOLOGY; MOLECULAR GENETICS; PROTEIN MOTIF; REPRODUCIBILITY; TIME;

EID: 3042666256     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh340     Document Type: Article
Times cited : (35199)

References (44)
  • 1
    • 0028679709 scopus 로고
    • On the complexity of multiple sequence alignment
    • Wang,L. and Jiang,T. (1994) On the complexity of multiple sequence alignment. J. Comput. Biol., 1, 337-348.
    • (1994) J. Comput. Biol. , vol.1 , pp. 337-348
    • Wang, L.1    Jiang, T.2
  • 3
    • 0021160693 scopus 로고
    • The alignment of sets of sequences and the construction of phyletic trees: An integrated method
    • Hogeweg,P. and Hesper,B. (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J. Mol. Evol., 20, 175-186.
    • (1984) J. Mol. Evol. , vol.20 , pp. 175-186
    • Hogeweg, P.1    Hesper, B.2
  • 4
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng,D.F. and Doolittle,R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-360.
    • (1987) J. Mol. Evol. , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 5
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. 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
  • 6
    • 0036208872 scopus 로고    scopus 로고
    • Recent progress in multiple sequence alignment: A survey
    • Notredame,C. (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenomics, 3, 131-144.
    • (2002) Pharmacogenomics , vol.3 , pp. 131-144
    • Notredame, C.1
  • 7
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • Gotoh,O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
    • (1996) J. Mol. Biol. , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 8
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh,K., Misawa,K., Kuma,K. and 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    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 9
    • 1242320272 scopus 로고    scopus 로고
    • Local homology recognition and distance measures in linear time using compressed amino acid alphabets
    • Edgar,R.C. (2004) Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res., 32, 380-385.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 380-385
    • Edgar, R.C.1
  • 12
    • 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
  • 13
    • 3042550791 scopus 로고    scopus 로고
    • A comparison of scoring functions for protein sequence profile alignment
    • DOI: 10.1093/bioinformatics/bth090
    • Edgar,R.C. and Sjolander,K. (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics, DOI: 10.1093/bioinformatics/bth090.
    • (2004) Bioinformatics
    • Edgar, R.C.1    Sjolander, K.2
  • 14
    • 0029906607 scopus 로고    scopus 로고
    • Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology
    • Sjolander,K., Karplus,K., Brown,M., Hughey,R., Krogh,A., Mian,I.S. and Haussler,D. (1996) Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. CABIOS, 12, 327-345.
    • (1996) CABIOS , vol.12 , pp. 327-345
    • Sjolander, K.1    Karplus, K.2    Brown, M.3    Hughey, R.4    Krogh, A.5    Mian, I.S.6    Haussler, D.7
  • 15
    • 84959053798 scopus 로고    scopus 로고
    • Improving profile-profile alignment via log average scoring
    • Gascuel,O. and Moret,B.M.E. (eds), Springer-Verlag, Berlin, Germany
    • von Ohsen,N. and Zimmer,R. (2001) Improving profile-profile alignment via log average scoring. In Gascuel,O. and Moret,B.M.E. (eds), Algorithms in Bioinformatics, First International Workshop, WABI 2001. Springer-Verlag, Berlin, Germany, pp. 11-26.
    • (2001) Algorithms in Bioinformatics, First International Workshop, WABI 2001 , pp. 11-26
    • von Ohsen, N.1    Zimmer, R.2
  • 16
    • 0036134748 scopus 로고    scopus 로고
    • Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
    • Muller,T., Spang,R. and Vingron,M. (2002) Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol. Biol. Evol., 19, 8-13.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 8-13
    • Muller, T.1    Spang, R.2    Vingron, M.3
  • 18
    • 0028928174 scopus 로고
    • Comprehensive study on iterative algorithms of multiple sequence alignment
    • Hirosawa,M., Totoki,Y., Hoshida,M. and Ishikawa,M. (1995) Comprehensive study on iterative algorithms of multiple sequence alignment. CABIOS, 11, 13-18.
    • (1995) CABIOS , vol.11 , pp. 13-18
    • Hirosawa, M.1    Totoki, Y.2    Hoshida, M.3    Ishikawa, M.4
  • 19
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (1999a) BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 20
    • 0035175770 scopus 로고    scopus 로고
    • BAliBASE (Benchmark Alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations
    • Bahr,A., Thompson,J.D., Thierry,J.C. and Poch,O. (2001) BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res., 29, 323-326.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 323-326
    • Bahr, A.1    Thompson, J.D.2    Thierry, J.C.3    Poch, O.4
  • 21
    • 3042613056 scopus 로고    scopus 로고
    • Align-m - A new algorithm for multiple alignment of highly divergent sequences
    • DOI: 10.1093/bioinformatics/bth116
    • Van Walle,I., Lasters,I. and Wyns,L. (2004) Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics, DOI: 10.1093/bioinformatics/bth116.
    • (2004) Bioinformatics
    • Van Walle, I.1    Lasters, I.2    Wyns, L.3
  • 22
    • 0032568655 scopus 로고    scopus 로고
    • SMART, a simple modular architecture research tool: Identification of signaling domains
    • Schultz,J., Milpetz,F., Bork,P. and Ponting,C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5857-5864
    • Schultz, J.1    Milpetz, F.2    Bork, P.3    Ponting, C.P.4
  • 24
    • 0032919370 scopus 로고    scopus 로고
    • SMART: Identification and annotation of domains from signalling and extracellular protein sequences
    • Ponting,C.P., Schultz,J., Milpetz,F. and Bork,P. (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 27, 229-332.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 229-332
    • Ponting, C.P.1    Schultz, J.2    Milpetz, F.3    Bork, P.4
  • 25
    • 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,J.D., Higgins,D.G. and Gibson,T.J. (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
    • hompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 26
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 27
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • urzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 28
    • 0028789439 scopus 로고
    • Optimal protein structure alignments by multiple linkage clustering: Application to distantly related proteins
    • Boutonnet,N.S., Rooman,M.J., Ochagavia,M.E., Richelle,J. and Wodak,S.J. (1995) Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Eng., 8, 647-662.
    • (1995) Protein Eng. , vol.8 , pp. 647-662
    • Boutonnet, N.S.1    Rooman, M.J.2    Ochagavia, M.E.3    Richelle, J.4    Wodak, S.J.5
  • 29
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 32
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignment algorithms with structure alignments
    • Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6-22.
    • (2000) Proteins , vol.40 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack Jr., R.L.3
  • 33
    • 0036211768 scopus 로고    scopus 로고
    • MaxBench: Evaluation of sequence and structure comparison methods
    • Leplae,R. and Hubbard,T.J. (2002) MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics, 18, 494-495.
    • (2002) Bioinformatics , vol.18 , pp. 494-495
    • Leplae, R.1    Hubbard, T.J.2
  • 34
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev,R. and Grishin,N. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
    • (2003) J. Mol. Biol. , vol.326 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 35
    • 2942544229 scopus 로고    scopus 로고
    • COACH: Profile-profile alignment of protein families using hidden Markov models
    • DOI: 10.1093/bioinformatics/bth091
    • Edgar,R.C. and Sjolander,K. (2004) COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics, DOI: 10.1093/bioinformatics/bth091.
    • (2004) Bioinformatics
    • Edgar, R.C.1    Sjolander, K.2
  • 36
    • 0031865006 scopus 로고    scopus 로고
    • Touring protein fold space with Dali/FSSP
    • Holm,L. and Sander,C. (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res., 26, 316-319.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 316-319
    • Holm, L.1    Sander, C.2
  • 39
    • 0037251892 scopus 로고    scopus 로고
    • NCBI Reference Sequence project: Update and current status
    • Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2003) NCBI Reference Sequence project: update and current status. Nucleic Acids Res., 31, 34-37.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 34-37
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 40
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (1999b) 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
  • 41
    • 3042661708 scopus 로고    scopus 로고
    • APDB: A novel measure for benchmarking sequence alignment methods without reference alignments
    • O'Sullivan,O., Zehnder,M., Higgins,D., Bucher,P., Grosdidier,A. and Notredame,C. (2003) APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics, 19 Suppl. 1, I215-I221.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • O'Sullivan, O.1    Zehnder, M.2    Higgins, D.3    Bucher, P.4    Grosdidier, A.5    Notredame, C.6
  • 42
    • 84944811700 scopus 로고
    • Tbe use of ranks to avoid the assumption of normality implicit in the analysis of variance
    • Friedman,M. (1937) Tbe use of ranks to avoid the assumption of normality implicit in the analysis of variance. J. Am. Stat. Assoc., 32, 675-701.
    • (1937) J. Am. Stat. Assoc. , vol.32 , pp. 675-701
    • Friedman, M.1
  • 43
    • 0031857684 scopus 로고    scopus 로고
    • Rose: Generating sequence families
    • Stoye,J., Evers,D. and Meyer,F. (1998) Rose: generating sequence families. Bioinformatics, 14, 157-163.
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 44
    • 0031604140 scopus 로고    scopus 로고
    • Phylogenetic inference in protein superfamilies: Analysis of SH2 domains
    • Sjolander,K. (1998) Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 165-174.
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.6 , pp. 165-174
    • Sjolander, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.