Protein sequence similarity searches using patterns as seeds

Nucleic Acids Research

Volumn 26, Issue 17, 1998, Pages 3986-3990

  Zhang, Zheng ^a   Schäffer, Alejandro A ^b   Miller, Webb ^a   Madden, Thomas L ^c   Lipman, David J ^c   Koonin, Eugene V ^c   Altschul, Stephen F ^c  

^a The Pennsylvania State University   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA PRIMASE; NUCLEOTIDYLTRANSFERASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DATA BASE; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE HOMOLOGY;

ARCHAEA;

EID: 0032169849     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/26.17.3986     Document Type: Article

References (54)

1. Smith, T.F. and Waterman, M.S. (1981) J. Mol. Biol., 147, 195-197.
2. Pearson, W.R. and Lipman, D.J. (1988) Proc. Natl Acad. Sci. USA, 85, 2444-2448.
3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) J. Mol. Biol., 215, 403-410.
4. Altschul, S.F. and Gish, W. (1996) Methods Enzymol., 266, 460-480.
5. Altschul, S.F., Madden, T.L., Schäffer,A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Nucleic Acids Res., 25, 3389-3402.
6. Myers, E.W. and Miller, W. (1989) Bull. Math. Biol., 51, 5-37.
7. Smith, R.F. and Smith, T.F. (1990) Proc. Natl Acad. Sci. USA, 87, 118-122.
8. Staden, R. (1990) Methods Enzymol., 183, 193-211.
9. Mehldau, G. and Myers, G. (1993) Comp. Appl. Biosci., 9, 299-314.
10. Tatusov, R.L. and Koonin, E.V. (1994) Comp. Appl. Biosci., 10, 457-459.
11. Ogiwara, A., Uchiyama, I., Takagi, T. and Kanehisa, M. (1996) Protein Sci., 5, 1991-1999.
12. Bairoch, A., Bucher, P. and Hofmann, K. (1997) Nucleic Acids Res., 25, 217-221.
13. Baeza-Yates,R. and Gonnet, G. (1992) Commun. Assoc. Comp. Mach., 35, 74-82.
14. Wu, S. and Manber, U. (1992) Commun. Assoc. Comp. Mach., 35, 83-91.
15. Sellers, P.H. (1984) Bull. Math. Biol., 46, 501-514.
16. Needleman, S.B. and Wunsch, C.D. (1970) J. Mol. Biol., 48, 443-453.
17. Sankoff, D. (1972) Proc. Natl Acad. Sci. USA, 69, 4-6.
18. Zhang, Z., Berman, P. and Miller, W. (1998) J. Comput. Biol., 5, 197-210.
19. Staden, R. (1989) Comp. Appl. Biosci., 5, 89-96.
20. Robinson, A.B. and Robinson, L.R. (1991) Proc. Natl Acad. Sci. USA. 88, 8880-8884.
21. Smith, T.F., Waterman, M.S. and Burks, C. (1985) Nucleic Acids Res., 13, 645-656.
22. Collins, J.F., Coulson, A.F.W. and Lyall, A. (1988) Comp. Appl. Biosci., 4, 67-71.
23. Mott, R. (1992) Bull. Math. Biol., 54, 59-75.
24. Waterman, M.S. and Vingron, M. (1994) Star. Sci., 9, 367-381.
25. Gumbel, E.J. (1958) Statistics of Extremes. Columbia University Press, New York, NY.
26. Pearson, W.R. (1998) J. Mol. Biol., 276, 71-84.
27. Henikoff, S. and Henikoff, J.G. (1992) Proc. Natl Acad. Sci. USA, 89, 10915-10919.
28. Wootton, J.C. and Federhen, S. (1993) Comp. Chem., 17, 149-163.
29. Altschul, S.F., Boguski, M.S., Gish, W. and Wootton, J.C. (1994) Nature Genet., 6, 119-129.
30. Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J. and Ouellette, B.F. (1998) Nucleic Acids Res., 26, 1-7.
31. Seshagiri, S. and Miller, L.K. (1997) Curr. Biol., 7, 455-460.
32. Chinnaiyan, A.M., Chaudhary, D., O'Rourke, K., Koonin, E.V. and Dixit, V.M. (1997) Nature, 388, 728-729.
33. Zou, H., Henzel, W.J., Liu, X., Lutschg, A. and Wang, X. (1997) Cell, 90, 405-113.
34. Li,P., Nijhawan,D., Budihardjo,I., Srinivasula,S.M., Ahmad,M., Alnemri, E.S. and Wang, X. (1997) Cell, 91, 479-489.
35. Buehler, E., Dewar, K., Feng, J., Kim, C., Li, Y., Shinn, P., Sun, H., Conway, A., Conway, A., Kurtz, D., et al. (1997) GenBank accession no. 2213598.
36. Bergerat, A., de Massy,B., Gadelle, D., Varoutas, P.C., Nicolas, A. and Forterre, P. (1997) Nature, 386, 414-417.
37. Mushegian, A.R., Bassett, D.E., Jr, Boguski,M.S., Bork, P. and Koonin, E.V. (1997) Proc. Natl Acad. Sci. USA, 94, 5831-5836.
38. Tsui, H.T., Mandavilli, B.S. and Winkler, M.E. (1992) Nucleic Acids Res., 20, 2379.
39. Wilson, R., Ainscough, R., Anderson, K., Baynes, C., Berks, M., Bonfield, J., Burton, J., Connell, M., Copsey, T., Cooper, J., et al. (1994) Nature, 368, 32-38.
40. Nagase, T., Seki, N., Tanaka, A., Ishikawa, K. and Nomura, N. (1995) DNA Res., 2, 167-174.
41. Bevan, M., Hilbert, H., Braun, M., Holzer, E., Brandt. A., Duesterhoeft, A., Hoheisel, J., Jesse, T., Heijnen, L., Vos, P., et al. (1998) GenBank accession no. 2961386.
42. Bevan, M., Hilbert, H., Braun, M., Holzer, E., Brandt. A., Duesterhoeft, A., Hoheisel, J., Jesse, T., Heijnen, L., Vos, P., et al. (1998) GenBank accession no. 2961387.
43. Yue, D., Maizels, N. and Weiner, A.M. (1996) RNA, 2, 895-908.
44. Dracheva, S., Koonin, E.V. and Crute, J. (1995) J. Biol. Chem., 270, 14148-14153.
45. Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., Sutton, G.G., Blake, J.A., FitzGerald, L.M., Clayton, R.A., Gocayne, J.D., et al. (1996) Science, 273, 1058-1073.
46. Klenk, H.P., Clayton, R.A., Tomb, J., White, O., Nelson, K.E., Ketchum, K.A., Dodson, R.J., Gwinn, M., Hickey, E.K., Peterson, J.D., et al. (1997) Nature, 390, 364-370.
47. Koonin, E.V., Mushegian, A.R., Galperin, M.Y. and Walker, D.R. (1997) Mol. Microbiol., 25, 619-637.
48. LeBlanc, D.J., Lee, L.N. and Inamine, J.M. (1991) Antimicrob. Agents Chemother., 35, 1804-1810.
49. Black, C.G., Fyfe, J.A. and Davies, J.K. (1995) J. Bacteriol., 177, 1952-1958.
50. Altschul, S.F. (1998) Proteins, 32, 88-96.
51. Gotoh, O. (1982) J. Mol. Biol., 162, 705-708.
52. Fitch, W.M. and Smith, T.F. (1983) Proc. Natl Acad. Sci. USA, 80, 1382-1386.
53. Altschul, S.F. and Erickson, B.W. (1986) Bull. Math. Biol., 48, 603-616.
54. Myers, E.W. and Miller, W. (1988) Comp. Appl. Biosci., 4, 11-17.