A general method for fast multiple sequence alignment

Gene

Volumn 172, Issue 1, 1996, Pages 33-41

  Tönges, Udo ^a   Perrey, Sören W ^b   Stoye, Jens ^a   Dress, Andreas W M ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b MASSEY UNIVERSITY   (New Zealand)

Author keywords

Divide and conquer; Dynamic programming; Multiple sequence alignment; Pair wise sequence alignment; Secondary matrix

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; GENETIC PROCEDURES; METHODOLOGY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

EID: 0029884395     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/0378-1119(96)00194-1     Document Type: Article

References (38)

1. Waterman, M.S. (1995) Introduction to Computational Biology. Maps Sequences and Genomes. Chapman & Hall, London.
2. Sankoff, D. and Kruskal, J.D, (editors) (1983) Time Warps, String Edits and Macro-molecules: The Theory and Practice of Sequence Comparison, Addison Wesley, Reading, MA.
3. Chan, S.C., Wong, A.K.C. and Chiu, D.K.Y. (1992) A survey of multiple sequence comparison methods. Bull. Math. Biol. 54(4): 563-598.
4. Myers, E.W. (1991) An overview of sequence comparison algorithms in molecular biology. Technical Report, TR 91-29, Department of Computer Science, University of Arizona, Tucson, AZ.
5. Murata, M., Richardson, J.S. and Sussman, J.L. (1985) Simultaneous comparison of three protein sequences. Proc. Natl. Acad. Sci. USA 82, 3073-3077.
6. Murata, M. (1990) Three-way Needleman-Wunsch algorithm. In: Doolittle, R.F. (ed.), Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, ch. 22, col. 183, Methods in Enzymology, Academic Press, San Diego, CA, pp. 365-375.
7. Carillo, H. and Lipman, D. (1988) The multiple sequence alignment problem in biology. SIAM J. Appl. Math. 48(5), 1073-1082.
8. Huang, X. (1993) Alignment of three sequences in quadratic space. Appl. Comput. Rev. 1(2), 7-11.
9. Allison, L. (1993) A fast algorithm for the optimal alignment of three strings. J.Theor. Biol. 164, 261-269.
10. Taylor, W.R. (1988) A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28, 161-169.
11. Higgins, D.G. and Sharp, P.M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
12. 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(22), 4673-4680.
13. Kececioglu, J. (1993) The maximum weight trace problem in multiple sequence alignment. In Proc. 4th Symp. Combinatorial Pattern Matching, LNCS 684, pp. 106-119.
14. Bafna, V., Lawler, E.L. and Pevzner, P.A. (1994) Approximation algorithms for multiple sequence alignment. In Proc. 5th Symp. Combinatorial Pattern Matching, LNCS 807, pp. 43-53.
15. Feng, D.F. and Doolittle, R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351-360.
16. Hirosawa, M., Hoshida, M., Ishikawa, M. and Toya, T. (1993) MASCOT: multiple alignment system for protein sequences based on three-Way dynamic programming. CABIOS 9(2), 161-167.
17. Johnson, M.S. and Doolittle, R.F. (1986) A method for the simultaneous alignment of three or more amino acid sequences. J. Mol. Evol. 23, 267-278.
18. Taylor, W.R. (1987) Multiple sequence alignment by a pairwise algorithm. CABIOS 3, 81-87.
19. Vingron, M. and Argos, P. (1991) Motif recognition and alignment for many sequences by comparison of dot-matrices. J. Mol. Biol. 218, 33-43.
20. Waterman, M.S. and Perlwitz, M. (1984) Line geometries for sequence comparisons. Bull. Math. Biol. 48, 189-195.
21. Altschul, S.F. (1989) Gap costs for multiple sequence alignment. J Theor. Biol. 138, 297-309.
22. Gotoh, O. (1986) Alignment of three biological sequences with an efficient traceback procedure. J. Theor. Biol. 121, 327-337, 1986.
23. 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.
24. Dress, A.W.M., Füllen, G. and Perrey, S.W. (1995) A divide and conquer approach to multiple alignment. In Proc. Third Conf. Intelligent Systems Mol. Biol., ISMB 95, AAAI Press, Menlo Park, CA, pp. 107-113.
25. Hirschberg, D.S. (1975) A linear space algorithm for computing maximal common subsequences. Commun. ACM 18(6), 341-343.
26. Vingron, M. and Argos, P. (1990) Determination of reliable regions in protein sequence alignments. Protein Eng. 3(7), 565-569.
27. Naor, D. and Brutlag, D.L. (1994) On near-optimal alignments of biological sequences. J. Comp. Biol. 1(4), 349-366.
28. Altschul, S.F., Carroll, R.J. and Lipman, D.J. (1989) Weights for data related by a tree. J. Mol. Biol. 207, 647-653.
29. Sibbald, P.R. and Argos, P. (1990) Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J. Mol. Biol. 216, 813-818.
30. Vingron, M. and Sibbald, P.R. (1993) Weighting in sequence space: a comparison of methods in terms of generalized sequences. Proc. Natl. Acad. Sci. USA 90, 8777-8781.
31. Lipman, D.J., Altschul, S.F. and Kececioglu, J.D. (1989) A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA 86, 4412-4415.
32. Gupta, S.K., Kececioglu, J.D. and Schäffer, A.A. (1995) Improving the practical space and time efficiency of the shortest-Paths approach to sum-of-pairs multiple sequence alignment. J. Comp. Biol. 2(3), 459-472.
33. Myers, E.W. and Miller, W. (1988) Optimal alignments in linear space. CABIOS 4(1), 11-17.
34. Wang, L. and Jiang, T. (1994) On the complexity of multiple sequence alignment. J. Comp. Biol. 1(4), 337-348.
35. Hein, J.J. (1990) Unified approach to alignment and phylogenies. In: Doolittle, R.F. (ed.), Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, ch. 39, vol. 183, Methods in Enzymology, Academic Press, San Diego, CA, pp. 626-645.
36. Bandelt, H.-J. and Barthelemy, J.P. (1984) Medians in median graphs. Discr. Appl. Math. 8, 131-142.
37. Sankoff, D., Cedergren, R.J. and LaPalme, G. (1976) Frequency of insertion-deletion, transversion and transition in the evolution of 5S ribosomal RNA. J. Mol. Biol. 7, 133-149.
38. Vingron, M. and von Haeseler, A. (1994) Towards integration of multiple alignment and phylogenetic tree reconstruction. Arbeitspapiere 852, GMD.