A non-local gap-penalty for profile alignment

Bulletin of Mathematical Biology

Volumn 58, Issue 1, 1996, Pages 1-18

  Taylor, William R ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBIN; HEMOGLOBIN; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; HUMAN; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; THEORETICAL MODEL;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; GLOBINS; HEMOGLOBINS; HUMANS; MODELS, THEORETICAL; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0029680109     PISSN: 00928240     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02458279     Document Type: Article

References (19)

1. Barton, G. J. and M. J. E. Sternberg, 1987a. Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng. 1, 89-94.
2. Barton, G. J. and M. J. E. Sternberg, 1987b. A strategy for the rapid multiple alignment of protein sequences. J. Mol. Biol. 198, 327-337.
3. Dayhoff, M. O., R. M. Schwartz and B. C. Orcutt, 1978. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure, M. O. Dayhoff (Ed), Vol. 5, Suppl. 3, pp. 345-352. Washington DC: Nat. Biomed. Res. Foundation.
4. Doolittle, R. F., D. F. Feng, M. S. Johnson and M. A. McClure, 1989. Origins and evolutionary relationships of retroviruses. Quart. Rev. Biol. 64, 1-30.
5. Feng, D. F. and R. F. Doolittle, 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351-360.
6. Gribskov, M., A. D. McLachlan and D. Eisenberg, 1987. Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. U.S.A. 84, 4355-4358.
7. Higgins, D. G. and P. M. Sharp, 1988. Clustal: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
8. Jones, D. T., W. R. Taylor and J. M. Thornton, 1992. A new approach to protein fold recognition. Nature 358, 86-89.
9. Lathrop, R. H. 1994. The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068.
10. Lesk, A., M. Levitt and C. Chothia, 1986. Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng. 1, 77-78.
11. McClure, M. A., T. K. Vasi and W. M. Fitch, 1994. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol. 11, 571-592.
12. Musacchio, A., T. J. Gibson, V. P. Lehto and M. Saraste. 1992. SH3 - an abundant protein domain in search of a function. FEBS Lett. 307, 55-61.
13. Needleman, S. B. and C. D. Wunsch, 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
14. Taylor, W. R. and C. A. Orengo, 1989. A protein structure alignment. J. Mol. Biol. 208, 1-22.
15. Taylor, W. R. 1988. A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28, 161-169.
16. Taylor, W. R. 1989. A template based method of pattern matching in protein sequences. Prog. Biophys. Mol. Biol. 54, 159-252.
17. Taylor, W. R. 1994. Motif-biased protein sequence alignment. J. Comp. Biol. 1.
18. Thompson, J. D., D. G. Higgins and T. J. Gibson, 1994a. 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.
19. Thompson, J. D., D. G. Higgins and T. J. Gibson, 1994b. Improved sensitivity of profile searches through the use of sequence weights and gap excision. CABIOS 10, 19-29.