Multiple protein sequence alignment using double-dynamic programming

Computers and Chemistry

Volumn 24, Issue 1, 2000, Pages 3-12

  Taylor, William R ^a,b   Sælensminde, Gisle ^b   Eidhammer, Ingvar ^b  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

Double dynamic programming; Multiple sequence alignment

Indexed keywords

FLAVODOXIN; GLOBIN; PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; SEQUENCE ALIGNMENT;

ALGORITHMS; FLAVODOXIN; GLOBINS; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0033631725     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(00)80003-0     Document Type: Article

References (27)

1. Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C., 1978. A model of evolutionary change in proteins. In: Dayhoff, M.O. (Ed.), Atlas of Protein Sequence and Structure, vol. 5. Nat. Biomed. Res. Foundation, Washington DC, pp. 345-352.
2. Holm, L., Sander, C., 1993. Protein-structure comparison by alignment of distance matrices. J. Molec. Biol. 233, 123-138.
3. Jonassen, I., Eidhammer, I., Taylor, W.R., 1999. Discovery of local packing motifs in protein structures. Proteins: Struc. Funct. Gene 34, 206-219.
4. Jones, D.T., Taylor, W.R., Thornton, J.M., 1992. A new approach to protein fold recognition. Nature 358, 86-89.
5. Kim, J., Pramanik, S., Chung, M.J., 1994. Multiple sequence alignment using simmulated annealing. Comp. App. Bio. Sci. 10, 419-426.
6. Lathrop, R.H., Smith, T.F., 1996. Global optimum protein threading with gapped alignment and empirical pair score functions. J. Molec. Biol. 255, 641-665.
7. Lathrop, R.H., 1994. The protein threading problem with sequence amino acid interaction preferences is NP-complete. Prot. Eng. 7, 1059-1068.
8. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., Wooton, J.C., 1993. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262, 208-214.
9. Needleman, S.B., Wunsch, C.D., 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Molec. Biol. 48, 443-453.
10. Notredame, C., Higgins, D.G., 1997. SAGA: sequence alignment by genetic algorithm. Nucleic Acids. Res. 24, 1515-1524.
11. Notredame, C., O'Brien, E.A., Higgins, D.G., 1997. RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids. Res. 25, 4570-4580.
12. Notredame, C., Holm, L., Higgins, D.G., 1998. COFFEE: an objective function for multiple sequence alignments. Bioinformation 14, 407-422.
13. Orengo, C.A., Taylor, W.R., 1990. A rapid method for protein structure alignment. J. Theor. Biol. 147, 517-551.
14. Smith, T.F., Waterman, M.S., 1981. Identification of common molecular subsequences. J. Molec. Biol. 147, 195-197.
15. Taylor, W.R., Munro, R.E.J., 1997. Multiple sequence threading: Conditional gap placement. Folding & Design 2, S33-S39.
16. Taylor, W.R., Orengo, C.A., 1989a. A holistic approach to protein structure comparison. Prot. Eng. 2, 505-519.
17. Taylor, W.R., Orengo, C.A., 1989b. Protein structure alignment. J. Molec. Biol. 208, 1-22.
18. Taylor, W.R., Flores, T.P., Orengo, C.A., 1994. Multiple protein structure alignment. Prot. Sci. 3, 1858-1870.
19. Taylor, W.R., 1987. Multiple sequence alignment by a pair-wise algorithm. Comp. App. Bio. Sci. 3, 81-87.
20. Taylor, W.R., 1988. A flexible method to align large numbers of biological sequences. J. Molec. Evol. 28, 161-169.
21. Taylor, W.R., 1990. Hierarchical method to align large numbers of biological sequences. In: Doolittle, R.F. (Ed.), Molecular Evolution: computer analysis of protein and nucleic acid sequences (Meth. Enzymol.), vol. 183. Academic Press, San Diego, CA, pp. 456-474.
22. Taylor, W.R., 1996. A non-local gap-penaly for profile alignment. Bull. Math. Biol. 58, 1-18.
23. Taylor, W.R., 1997a. Multiple sequence threading: an analysis of alignment quality and stability. J. Molec. Biol. 269, 902-943.
24. Taylor, W.R., 1997b. Residual colours: a proposal for aminochromography. Prot. Eng. 10, 743-746.
25. Taylor, W.R., 1999a. The properties of amino acids in sequences. In: Bishop, M.J., (Ed.), Nucleic acid and protein databases: a practical approach (second edition), Practical approach (Rickwood, D., Hames, B.D. (Eds.)). IRL Press, Oxford, Chapter 5, pp. 81-103.
26. Taylor, W.R., 1999b. Protein structure alignment using iterated double dynamic programming. Prot. Sci. 8, 654-665.
27. Sali, A., Blundell, T.L., 1990. Definition of general topological equivalence in protein structures: a procedure involving comparison of properties and relationship through simulated annealing and dynamic programming. J. Molec. Biol. 212, 403-428.