메뉴 건너뛰기




Volumn 26, Issue 8, 2010, Pages 1015-1021

A min-cut algorithm for the consistency problem in multiple sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DNA SEQUENCE; GENETIC DATABASE; GENOMICS; METHODOLOGY; SEQUENCE ALIGNMENT;

EID: 77951942339     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq082     Document Type: Article
Times cited : (22)

References (38)
  • 1
    • 23044525766 scopus 로고    scopus 로고
    • Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB)
    • Abdeddaïm,S. and Morgenstern,B. (2001) Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB). Lect. Notes Comput. Sci., 2066, 1-11.
    • (2001) Lect. Notes Comput. Sci. , vol.2066 , pp. 1-11
    • Abdeddaïm, S.1    Morgenstern, B.2
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLASTand PSI-BLAST: a new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 4
    • 0004116989 scopus 로고    scopus 로고
    • MIT Press, Cambridge, MA; London, England
    • Cormen,T. et al. (2001) Introduction to Algorithms. MIT Press, Cambridge, MA; London, England.
    • (2001) Introduction to Algorithms
    • Cormen, T.1
  • 5
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: probabilistic consistency-based multiple sequence alignment
    • Do,C.B. et al. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
    • (2005) Genome Res. , vol.15 , pp. 330-340
    • Do, C.B.1
  • 7
    • 60749103932 scopus 로고    scopus 로고
    • Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins
    • Dress,A. et al. (2008) Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins. Algorithms Mol. Biol., 3, 15.
    • (2008) Algorithms Mol. Biol. , vol.3 , pp. 15
    • Dress, A.1
  • 9
    • 0000994187 scopus 로고
    • Fast and sound two-step algorithms for multiple alignment of nucleic sequences
    • AAAI Press, Atlanta
    • Eddy,S. (1995) Fast and sound two-step algorithms for multiple alignment of nucleic sequences. In Proceedings of Intelligent Systems for Molecular Biology '95. AAAI Press, Atlanta, pp. 114-120.
    • (1995) In Proceedings of Intelligent Systems for Molecular Biology '95 , pp. 114-120
    • Eddy, S.1
  • 10
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high score accuracy and high throughput
    • Edgar,R. (2004) MUSCLE: multiple sequence alignment with high score accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.1
  • 12
    • 0015330635 scopus 로고
    • Theoretical improvements in algorithmic efficiency for network flow problems
    • Edmonds,J. and Karp,R.M. (1972) Theoretical improvements in algorithmic efficiency for network flow problems. J. ACM, 19, 248-264.
    • (1972) J. ACM , vol.19 , pp. 248-264
    • Edmonds, J.1    Karp, R.M.2
  • 13
    • 0001261128 scopus 로고
    • Maximal flow through a network
    • Ford,L. and Fulkerson,D. (1956) Maximal flow through a network. Can. J. Math, 8, 399-404.
    • (1956) Can. J. Math , vol.8 , pp. 399-404
    • Ford, L.1    Fulkerson, D.2
  • 14
    • 0025138774 scopus 로고
    • Consistency of optimal sequence alignments
    • Gotoh,O. (1990) Consistency of optimal sequence alignments. Bull. Math. Biol., 52, 509-525.
    • (1990) Bull. Math. Biol. , vol.52 , pp. 509-525
    • Gotoh, O.1
  • 16
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh,K.et al. (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
  • 17
    • 0003321583 scopus 로고    scopus 로고
    • A polyhedral approach to sequence alignment problems
    • Kececioglu,J.D. et al. (2000) A polyhedral approach to sequence alignment problems. Discrete Appl. Math., 104, 143-186.
    • (2000) Discrete Appl. Math. , vol.104 , pp. 143-186
    • Kececioglu, J.D.1
  • 18
    • 70349866695 scopus 로고    scopus 로고
    • Upcoming challenges for multiple sequence alignment methods in the high-throughput era
    • Kemena,C. and Notredame,C. (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
    • (2009) Bioinformatics , vol.25 , pp. 2455-2465
    • Kemena, C.1    Notredame, C.2
  • 19
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann,T. and Sonnhammer,E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett., 529, 126-130.
    • (2002) FEBS Lett. , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 20
    • 29244447181 scopus 로고    scopus 로고
    • Kalign an accurate and fast multiple sequence alignment algorithm
    • Lassmann,T. and Sonnhammer,E.L. (2005) Kalign an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics, 6, 298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 298
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 21
    • 0032892093 scopus 로고    scopus 로고
    • An exact solution for the segment-to-segment multiple sequence alignment problem
    • Lenhof,H.-P. et al. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics, 15, 203-210.
    • (1999) Bioinformatics , vol.15 , pp. 203-210
    • Lenhof, H.-P.1
  • 22
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2 improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern,B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211-218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 23
    • 0033636013 scopus 로고    scopus 로고
    • A space-efficient algorithm for aligning large genomic sequences
    • Morgenstern,B. (2000) A space-efficient algorithm for aligning large genomic sequences. Bioinformatics, 16, 948-949.
    • (2000) Bioinformatics , vol.16 , pp. 948-949
    • Morgenstern, B.1
  • 24
    • 31244432403 scopus 로고    scopus 로고
    • A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
    • Morgenstern,B. (2002) A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences. Appl. Math. Lett., 15, 11-16.
    • (2002) Appl. Math. Lett. , vol.15 , pp. 11-16
    • Morgenstern, B.1
  • 25
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern,B. et al. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1
  • 26
    • 16344379173 scopus 로고    scopus 로고
    • Multiple sequence alignment with user-defined constraints at GOBICS
    • Morgenstern,B. et al. (2005) Multiple sequence alignment with user-defined constraints at GOBICS. Bioinformatics, 21, 1271-1273.
    • (2005) Bioinformatics , vol.21 , pp. 1271-1273
    • Morgenstern, B.1
  • 27
    • 34248363117 scopus 로고    scopus 로고
    • Multiple sequence alignment with user-defined anchor points
    • Morgenstern,B. et al. (2006) Multiple sequence alignment with user-defined anchor points. Algorithms Mol. Biol., 1,6.
    • (2006) Algorithms Mol. Biol. , vol.1 , pp. 6
    • Morgenstern, B.1
  • 28
    • 33845727469 scopus 로고    scopus 로고
    • Multiple sequence alignment for phylogenetic purposes
    • Morrison,D.A. (2006) Multiple sequence alignment for phylogenetic purposes. Aust. Syst. Bot., 19, 479-539.
    • (2006) Aust. Syst. Bot. , vol.19 , pp. 479-539
    • Morrison, D.A.1
  • 29
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 30
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: a novel algorithm for multiple sequence alignment
    • Notredame, C., Higgins, D., and Heringa, J. (2000). T-Coffee: a novel algorithm for multiple sequence alignment. J. Mol. Biol., 302, 205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.2    Heringa, J.3
  • 32
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 33
    • 0031857684 scopus 로고    scopus 로고
    • Rose: generating sequence families
    • Stoye,J. et al. (1998) Rose: generating sequence families. Bioinformatics, 14, 157-163.
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1
  • 34
    • 20444489707 scopus 로고    scopus 로고
    • DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment
    • Subramanian,A.R. et al. (2005) DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics, 6, 66.
    • (2005) BMC Bioinformatics , vol.6 , pp. 66
    • Subramanian, A.R.1
  • 35
    • 45949105543 scopus 로고    scopus 로고
    • DIALIGN-TX: greedy and progressive approaches for the segment-based multiple sequence alignment
    • Subramanian,A.R. et al. (2008) DIALIGN-TX: greedy and progressive approaches for the segment-based multiple sequence alignment. Algorithms Mol. Biol., 3,6.
    • (2008) Algorithms Mol. Biol. , vol.3 , pp. 6
    • Subramanian, A.R.1
  • 36
    • 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. et al. (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
  • 37
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3 0: latest developments of the multiple sequence alignment benchmark
    • Thompson,J.D. et al. (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins Struct. Funct. Bioinform., 61, 127-136.
    • (2005) Proteins Struct. Funct. Bioinform. , vol.61 , pp. 127-136
    • Thompson, J.D.1
  • 38
    • 0026036377 scopus 로고
    • Motif recognition and alignment for many sequences by comparison of dot-matrices
    • Vingron,M. and Argos,P. (1991) Motif recognition and alignment for many sequences by comparison of dot-matrices. J. Mol. Biol., 218, 33-43.
    • (1991) J. Mol. Biol. , vol.218 , pp. 33-43
    • Vingron, M.1    Argos, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.