메뉴 건너뛰기




Volumn 104, Issue 1-3, 2000, Pages 143-186

A polyhedral approach to sequence alignment problems

Author keywords

Branch and cut; Combinatorial optimization; Computational biology; Multiple sequence alignment; RNA sequence alignment

Indexed keywords


EID: 0003321583     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-218X(00)00194-3     Document Type: Article
Times cited : (39)

References (41)
  • 1
    • 0022885515 scopus 로고
    • Locally optimal subalignments using nonlinear similarity functions
    • Altschul S.F., Erickson B.W. Locally optimal subalignments using nonlinear similarity functions. Bull. Math. Biol. 48:1986;633-660.
    • (1986) Bull. Math. Biol. , vol.48 , pp. 633-660
    • Altschul, S.F.1    Erickson, B.W.2
  • 3
    • 33846647635 scopus 로고
    • Computing similarity between RNA strings
    • Z. Galil, & E. Ukkonen. Proceedings of the Sixth Annual Symposium on Combinatorial Pattern Matching (CPM-95). Berlin: Springer
    • Bafna V., Muthukrishnan S., Ravi R. Computing similarity between RNA strings. Galil Z., Ukkonen E. Proceedings of the Sixth Annual Symposium on Combinatorial Pattern Matching (CPM-95). Lecture Notes in Computer Science. Vol. 937:1995;1-16 Springer, Berlin.
    • (1995) Lecture Notes in Computer Science , vol.937 , pp. 1-16
    • Bafna, V.1    Muthukrishnan, S.2    Ravi, R.3
  • 4
    • 0027982394 scopus 로고
    • RNAlign program: Alignment of RNA sequences using both primary and secondary structures
    • Corpet F., Michot B. RNAlign program: alignment of RNA sequences using both primary and secondary structures. CABIOS. 10(4):1994;389-399.
    • (1994) CABIOS , vol.10 , Issue.4 , pp. 389-399
    • Corpet, F.1    Michot, B.2
  • 5
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • M.O. Dayhoff. Washington, DC: National Biomedical Research Foundation
    • Dayhoff M.O., Schwartz R.M., Orcut B.C. A model of evolutionary change in proteins. Dayhoff M.O. Atlas of Proteins Sequence and Structure, Vol. 5. 1979;345-352 National Biomedical Research Foundation, Washington, DC.
    • (1979) Atlas of Proteins Sequence and Structure, Vol. 5 , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcut, B.C.3
  • 7
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy S.R., Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 22(11):1994;2079-2088.
    • (1994) Nucleic Acids Res. , vol.22 , Issue.11 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 8
    • 0030812919 scopus 로고    scopus 로고
    • Finding the most significant common sequence and structure motifs in a set of RNA sequences
    • Gorodkin J., Heyer L.J., Stormo G.D. Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res. 25:1997;3724-3732.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3724-3732
    • Gorodkin, J.1    Heyer, L.J.2    Stormo, G.D.3
  • 9
    • 0021521702 scopus 로고
    • A cutting plane algorithm for the linear ordering problem
    • Grötschel M., Jünger M., Reinelt G. A cutting plane algorithm for the linear ordering problem. Oper. Res. 32:1984;1195-1220.
    • (1984) Oper. Res. , vol.32 , pp. 1195-1220
    • Grötschel, M.1    Jünger, M.2    Reinelt, G.3
  • 10
    • 51249185617 scopus 로고
    • The ellipsoid method and its consequences in combinatorial optimization
    • Grötschel M., Lovász L., Schrijver A. The ellipsoid method and its consequences in combinatorial optimization. Combinatorica. 1:1981;169-197.
    • (1981) Combinatorica , vol.1 , pp. 169-197
    • Grötschel, M.1    Lovász, L.2    Schrijver, A.3
  • 12
    • 0029366816 scopus 로고
    • Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment
    • Gupta S.K., Kececioglu J.D., Schaeffer A.A. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J. Comput. Biol. 2:1995;459-472.
    • (1995) J. Comput. Biol. , vol.2 , pp. 459-472
    • Gupta, S.K.1    Kececioglu, J.D.2    Schaeffer, A.A.3
  • 14
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • 915-10 919
    • Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Nat. Acad. Sci. USA. 89:1992;10 915-10 919.
    • (1992) Proc. Nat. Acad. Sci. USA , vol.89 , pp. 10
    • Henikoff, S.1    Henikoff, J.G.2
  • 15
    • 77957083042 scopus 로고
    • The traveling salesman problem
    • M. Ball, T. Magnanti, C.L. Monma, & G.L. Nemhauser. North Holland: Elsevier
    • Jünger M., Reinelt G., Rinaldi G. The traveling salesman problem. Ball M., Magnanti T., Monma C.L., Nemhauser G.L. Handbook on Operations Research and Management Science. 1995;225-330 Elsevier, North Holland.
    • (1995) Handbook on Operations Research and Management Science , pp. 225-330
    • Jünger, M.1    Reinelt, G.2    Rinaldi, G.3
  • 17
    • 4243258421 scopus 로고    scopus 로고
    • The design of the branch and cut system ABACUS
    • Institut für Informatik, Universität zu Köln
    • M. Jünger, S. Thienel, The design of the branch and cut system ABACUS, Technical Report 97.260, Institut für Informatik, Universität zu Köln, 1997.
    • (1997) Technical Report 97.260
    • Jünger, M.1    Thienel, S.2
  • 18
    • 0005314510 scopus 로고
    • On linear characterizations of combinatorial optimization problems
    • Karp R.M., Papadimitriou C.H. On linear characterizations of combinatorial optimization problems. SIAM J. Comput. 11:1982;620-632.
    • (1982) SIAM J. Comput. , vol.11 , pp. 620-632
    • Karp, R.M.1    Papadimitriou, C.H.2
  • 22
    • 0345865548 scopus 로고    scopus 로고
    • * algorithm for exact multiple sequence alignment
    • Max-Planck-Institut für Informatik, Saarbrücken
    • * algorithm for exact multiple sequence alignment, Research report MPI-I-97-1-028, Max-Planck-Institut für Informatik, Saarbrücken, 1997.
    • (1997) Research Report MPI-I-97-1-028
    • Lermen, M.1    Reinert, K.2
  • 23
    • 0014688034 scopus 로고
    • Detailed molecular model for transfer ribonucleic acid
    • Levitt M. Detailed molecular model for transfer ribonucleic acid. Nature. 224:1969;759-763.
    • (1969) Nature , vol.224 , pp. 759-763
    • Levitt, M.1
  • 24
    • 0028341506 scopus 로고
    • Comparative analysis of multiple protein-sequence alignment methods
    • McClure M.A., Vasi T.K., Fitch W.M. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol. 11(4):1994;571-592.
    • (1994) Mol. Biol. Evol. , vol.11 , Issue.4 , pp. 571-592
    • McClure, M.A.1    Vasi, T.K.2    Fitch, W.M.3
  • 25
    • 0029184961 scopus 로고
    • LEDA, a platform for combinatorial and geometric computing
    • Mehlhorn K., Näher S. LEDA, a platform for combinatorial and geometric computing. Commun. ACM. 38(1):1995;96-102.
    • (1995) Commun. ACM , vol.38 , Issue.1 , pp. 96-102
    • Mehlhorn, K.1    Näher, S.2
  • 27
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • 098-12 103
    • Morgenstern B., Dress A., Werner T. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Nat. Acad. Sci. 93:1996;12 098-12 103.
    • (1996) Proc. Nat. Acad. Sci. , vol.93 , pp. 12
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 28
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino-acid sequence of two proteins
    • Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino-acid sequence of two proteins. J. Mol. Biol. 48:1970;443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 30
    • 0016028005 scopus 로고
    • Properties of vertex packing and independence system polyhedra
    • Nemhauser G.L., Trotter L.E. Properties of vertex packing and independence system polyhedra. Math. Programming. 6:1973;48-61.
    • (1973) Math. Programming , vol.6 , pp. 48-61
    • Nemhauser, G.L.1    Trotter, L.E.2
  • 32
    • 0023313723 scopus 로고
    • Optimization of a 532 city symmetric traveling salesman problem by branch and cut
    • Padberg M.W., Rinaldi G. Optimization of a 532 city symmetric traveling salesman problem by branch and cut. Oper. Res. Lett. 6:1987;1-7.
    • (1987) Oper. Res. Lett. , vol.6 , pp. 1-7
    • Padberg, M.W.1    Rinaldi, G.2
  • 33
    • 0039631231 scopus 로고
    • Generalized sequence alignment and duality
    • Pevzner P.A., Waterman M.S. Generalized sequence alignment and duality. Adv. Appl. Math. 14:1993;139-171.
    • (1993) Adv. Appl. Math. , vol.14 , pp. 139-171
    • Pevzner, P.A.1    Waterman, M.S.2
  • 34
    • 0345865535 scopus 로고    scopus 로고
    • Ph.D. Thesis Universität des Saarlandes, Im Stadtwald, 66123 Saarbrücken, Germany
    • K. Reinert, A polyhedral approach to sequence alignment problems, Ph.D. Thesis Universität des Saarlandes, Im Stadtwald, 66123 Saarbrücken, Germany, 1999.
    • (1999) A Polyhedral Approach to Sequence Alignment Problems
    • Reinert, K.1
  • 35
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 45(5):1985;810-825.
    • (1985) SIAM J. Appl. Math. , vol.45 , Issue.5 , pp. 810-825
    • Sankoff, D.1
  • 38
    • 0001228780 scopus 로고
    • A new algorithm for generating all the maximal independent sets
    • Tsukiyama S., Ide M., Ariyoshi H., Shirawaka I. A new algorithm for generating all the maximal independent sets. SIAM J. Comput. 6:1977;505-517.
    • (1977) SIAM J. Comput. , vol.6 , pp. 505-517
    • Tsukiyama, S.1    Ide, M.2    Ariyoshi, H.3    Shirawaka, I.4
  • 39
    • 0009603933 scopus 로고
    • Multiple sequence comparison and consistency on multipartite graphs
    • Vingron M., Pevzner P. Multiple sequence comparison and consistency on multipartite graphs. Adv. Appl. Math. 16:1995;1-22.
    • (1995) Adv. Appl. Math. , vol.16 , pp. 1-22
    • Vingron, M.1    Pevzner, P.2
  • 40
    • 0039080150 scopus 로고
    • Consensus methods for folding single-stranded nucleic acids
    • CRC Press, Boca Raton, FL
    • M.S. Waterman, Consensus methods for folding single-stranded nucleic acids, Mathematical Methods for DNA Sequences, CRC Press, Boca Raton, FL, 1989, pp. 185-224.
    • (1989) Mathematical Methods for DNA Sequences , pp. 185-224
    • Waterman, M.S.1
  • 41
    • 0021451172 scopus 로고
    • The context dependent comparison of biological sequences
    • Wilbur W.J., Lipman D.J. The context dependent comparison of biological sequences. SIAM J. Appl. Math. 44(3):1984;557-567.
    • (1984) SIAM J. Appl. Math. , vol.44 , Issue.3 , pp. 557-567
    • Wilbur, W.J.1    Lipman, D.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.