CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Nucleic Acids Research

Volumn 22, Issue 22, 1994, Pages 4673-4680

  Thompson, Julie D ^a   Higgins, Desmond G ^a   Gibson, Toby J ^a  

^a Europ Molec Biology Organization   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBIN; PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER PROGRAM; HYDROPHILICITY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPARATIVE STUDY; GLOBINS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0027968068     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/22.22.4673     Document Type: Article

References (40)

1. Feng, D.-F and Doolittle, R.F. (1987) J. Mol. Evol. 25, 351-360.
2. Needleman, S.B and Wunsch, CD. (1970) J. Mol. Biol. 48, 443-453.
3. Dayhoff, M.O., Schwartz, R.M and Orcutt, B.C. (1978) In Atlas of Protein Sequence and Structure, vol. 5, suppl. 3 (Dayhoff, M.O., ed.), pp 345-352. NBRF, Washington.
4. Henikoff, S and Henikoff, J.G. (1992) Proc. Natl. Acad. Sci. USA 89, 10915-10919.
5. Lipman, D.J., Altschul, S.F and Kececioglu, J.D. (1989) Proc. Natl. Acad. Sci. USA 86, 4412-4415.
6. Barton, G.J and Sternberg, M.J.E. (1987) J. Mol. Biol. 198, 327-337.
7. Gotoh, O. (1993) CABIOS 9, 361-370.
8. Altschul, S.F. (1989) J. Theor. Biol. 138, 297-309.
9. Lukashin, A.V., Engelbrecht, J and Brunak, S. (1992) Nucleic Acids Res. 20, 2511-2516.
10. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu J.S, Neuwald, A.F and Wooton, J.C. (1993) Science 262, 208-214.
11. Vingron, M and Waterman, M.S. (1993) J. Mol. Biol. 234, 1-12.
12. Pascarella, S and Argos, P. (1992) J. Mol. Biol. 224, 461-471.
13. Collins, J.F and Coulson, A.F.W. (1987) In Nucleic Acid and Protein Sequence Analysis, A Practical Approach (Bishop, M.J and Rawlings, C.J., eds), chapter 13, pp. 323-358.
14. Vingron, M and Sibbald, P.R. (1993) Proc. Natl. Acad. Sci. USA 90, 8777-8781.
15. Thompson, J.D., Higgins, D.G and Gibson, T.J. (1994) CABIOS 10, 19-29.
16. Liithy, R., Xenarios, I and Bucher, P. (1994) Protein Sci. 3, 139-146.
17. Higgins, D.G and Sharp, P.M. (1988) Gene 73, 237-244.
18. Higgins, D.G and Sharp, P.M. (1989) CABIOS 5, 151-153.
19. Higgins, D.G., Bleasby, A.J and Fuchs, R. (1992) CABIOS 8, 189-191.
20. Sneath, P.H.A and Sokal, R.R. (1973) Numerical Taxonomy. W.H. Freeman, San Francisco.
21. Saitou, N and Nei, M. (1987) Mol. Biol. Evol. 4, 406-425.
22. Bashford, D., Chothia, C and Lesk, A.M. (1987) J. Mol. Biol. 196, 199-216.
23. Musacchio, A., Gibson, T., Lento, V.-P and Saraste, M. (1992). FEBS Lett. 307, 55-61.
24. Musacchio, A., Noble, M., Pauptit, R., Wierenga, R and Saraste, M. (1992). Nature, 359, 851-855.
25. Bashford, D., Chothia, C and Lesk, A.M. (1987). J. Mol. Biol. 196, 199-216.
26. Myers, E.W and Miller, W. (1988). CABIOS 4, 11-17.
27. Thompson, J.D. (1994). CABIOS submitted for publication.
28. Smith, T.F., Waterman, M.S and Fitch, W.M. (1981) J. Mol. Evol. 18, 38-46.
29. Pearson, W.R and Lipman, D.J. (1988) Proc. Natl. Acad. Sci. USA. 85, 2444-2448.
30. Devereux, J., Haeberli, P and Smithies, O. (1984) Nucleic Acids Res. 12, 387-395.
31. Felsenstein, J. (1989) Cladistics 5, 164-166.
32. Kimura, M. (1980) J. Mol. Evol. 16, 111-120.
33. Kimura, M. (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
34. Felsenstein, J. (1985) Evolution 39, 783-791.
35. Smith, R.F and Smith, T.F. (1992) Protein Engng 5, 35-41.
36. Krogh, A., Brown, M., Mian, S., Sjolander, K and Haussler, D. (1994) J. Mol. Biol. 235-1501-1531.
37. Jones, D.T., Taylor, W.R and Thornton, J.M. (1994) FEBS Lett. 339, 269-275.
38. Bairoch, A and Bockmann, B. (1992) Nucleic Acids Res. 20, 2019-2022.
39. Noble, M.E.M., Musacchio, A., Saraste, M., Courtneidge, S.A and Wierenga, R.K. (1993) EMBO J. 12, 2617-2624.
40. Kabsch, W and Sander, C. (1983) Biopolymers 22, 2577-2637.