Gapped BLAST and PSI-BLAST: A new generation of protein database search programs

Nucleic Acids Research

Volumn 25, Issue 17, 1997, Pages 3389-3402

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

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; COMPUTER PROGRAM; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; TECHNIQUE;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; DATABASES, FACTUAL; DNA; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0030801002     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.17.3389     Document Type: Review

References (90)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) J. Mol. Biol., 215, 403-410.
2. Pearson, W.R. and Lipman, D.J. (1988) Proc. Natl. Acad. Sci. USA, 85, 2444-2448.
3. Altschul, S.F. and Gish, W. (1996) Methods Enzymol., 266, 460-480.
4. Chao, K.-M., Pearson, W.R. and Miller, W. (1992) Comput. Appl. Biosci., 8, 481-487.
5. Sellers, P.H. (1984) Bull. Math. Biol., 46, 501-514.
6. Altschul, S.F. and Erickson, B.W. (1986) Bull. Math. Biol., 48, 633-660.
7. Waterman, M.S. and Eggert, M. (1987) J. Mol. Biol., 197, 723-728.
8. Karlin, S. and Altschul, S.F. (1990) Proc. Natl. Acad. Sci. USA, 87, 2264-2268.
9. Dembo, A., Karlin, S. and Zeitouni, O. (1994) Ann. Prob., 22, 2022-2039.
10. Altschul, S.F. (1991) J. Mol. Biol., 219, 555-565.
11. Altschul, S.F. (1993) J. Mol. Evol., 36, 290-300.
12. Smith, T.F., Waterman, M.S. and Burks, C. (1985) Nucleic Acids Res., 13, 645-656.
13. Collins, J.F., Coulson, A.F.W. and Lyall, A. (1988) Comput. Appl. Biosci., 4, 67-71.
14. Mott, R. (1992) Bull. Math. Biol., 54, 59-75.
15. Waterman, M.S. and Vingron, M. (1994) Stat. Sci., 9, 367-381.
16. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, Suppl. 3, pp. 345-352.
17. Schwartz, R.M. and Dayhoff, M.O. (1978) In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, Suppl. 3, pp. 353-358.
18. Henikoff, S. and Henikoff, J.G. (1992) Proc. Natl. Acad. Sci. USA, 89, 10915-10919.
19. Wilbur, W.J. and Lipman, D.J. (1983) Proc. Natl. Acad. Sci. USA, 80, 726-730.
20. Robinson, A.B. and Robinson, L.R. (1991) Proc. Natl. Acad. Sci. USA, 88, 8880-8884.
21. Karlin, S. and Altschul, S.F. (1993) Proc. Natl. Acad. Sci. USA, 90, 5873-5877.
22. Altschul, S.F. (1997) In Suhai, S. (ed.), Theoretical and Computational Methods in Genome Research. Plenum Press, New York, pp. 1-14.
23. Needleman, S.B. and Wunsch, C.D. (1970) J. Mol. Biol., 48, 443-453.
24. Smith, T.F. and Waterman, M.S. (1981) J. Mol. Biol., 147, 195-197.
25. Sankoff, D. and Kruskal, J.B. (1983) Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, MA.
26. Bairoch, A. and Apweiler, R. (1997) Nucleic Acids Res., 25, 31-36.
27. Jou, W.M., Verhoeyen, M., Devos, R., Saman, E., Fang, R., Huylebroeck, D., Fiers, W., Threlfall, G., Barber, C., Carey, N. and Emtage, S. (1980) Cell, 19, 683-696.
28. McLachlan, A.D. (1983) J. Mol. Biol., 169, 15-30.
29. Staden, R. (1984) Nucleic Acids Res., 12, 505-519.
30. Schneider, T.S., Stormo, G.D., Gold, L. and Ehrenfeucht, A. (1986) J. Mol. Biol., 188, 415-431.
31. Taylor, W.R. (1986). J. Mol. Biol., 188, 233-258.
32. Berg, O.G. and von Hippel, P.H. (1987) J. Mol. Biol. 193, 723-750.
33. Dodd, I.B. and Egan, J.B. (1987) J. Mol. Biol., 194, 557-564.
34. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Proc. Natl. Acad. Sci. USA, 84, 4355-4358.
35. Patthy, L. (1987) J. Mol. Biol., 198, 567-577.
36. Stormo, G.D. and Hartzell, G.W. III (1989) Proc. Natl. Acad. Sci. USA, 86, 1183-1187.
37. Tatusov, R.L., Altschul, S.F. and Koonin, E.V. (1994) Proc. Natl. Acad. Sci. USA, 91, 12091-12095.
38. Yi, T.-M. and Lander, E.S. (1994) Protein Sci., 3, 1315-1328.
39. Henikoff, S. and Henikoff, J.G. (1997) Protein Sci., 6, 698-705.
40. Bucher, P., Karplus, K., Moeri, N. and Hofmann, K. (1996) Comput. Chem., 20, 3-23.
41. Sellers, P.H. (1980) J. Algorithms, 1, 359-373.
42. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Science, 262, 208-214.
43. Altschul, S.F., Carroll, R.J. and Lipman, D.J. (1989) J. Mol. Biol., 207, 647-653.
44. Sibbald, P.R. and Argos, P. (1990) J. Mol. Biol., 216, 813-818.
45. Sander, C. and Schneider, R. (1991) Proteins, 9, 56-68.
46. Gerstein, M., Sonnhammer, E.L. and Chothia, C. (1994) J. Mol. Biol. 236, 1067-1078.
47. Henikoff, S. and Henikoff, J.G. (1994) J. Mol. Biol., 243, 574-578.
48. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Comput. Appl. Biosci., 10, 19-29.
49. Eddy, S.R., Mitchison, G. and Durbin, R. (1995) J. Comput. Biol., 2, 9-23.
50. Gotoh, O. (1995) Comput. Appl. Biosci., 11, 543-551.
51. Krogh, A. and Mitchison, G. (1995) In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S. (eds.), Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 215-221.
52. Henikoff, J.G. and Henikoff, S. (1996) Comput. Appl. Biosci., 12, 135-143.
53. Brown, M, Hughey, R., Krogh, A., Mian, I.S., Sjölander, K. and Haussler, D. (1993) In Hunter, L., Searls, D. and Shavlik, J. (eds.), Proceedings of the First International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 47-55.
54. Bailey, T.L. and Gribskov, M. (1996) In States, D.J., Agarwal, P., Gaasterland, T., Hunter, L. and Smith, R. (eds.), Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 15-24.
55. Karplus, K. (1995) In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S. (eds.), Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 188-196.
56. Sjölander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I.S. and Haussler, D. (1996) Comput. Appl. Biosci., 12, 327-345.
57. Wootton, J.C. and Federhen, S. (1993) Comput. Chem., 17, 149-163.
58. Altschul, S.F., Boguski, M.S., Gish, W. and Wootton, J.C. (1994) Nature Genet., 6, 119-129.
59. Benson, D.A., Boguski, M.S., Lipman, D.J. and Ostell, J. (1997) Nucleic Acids Res., 25, 1-6.
60. Holm, L. and Sander, C. (1997) Structure, 5, 165-171.
61. Ohta, M., Inoue, H., Cotticelli, M.G., Kastury, K., Baffa, R., Palazzo, J., Siprashvili, Z., Mori, M., McCue, P., Druck, T., Croche, C.M. and Huebner, K. (1996) Cell, 84, 587-597.
62. Heidenreich, R.A., Mallee, J. and Segal, S. (1993) DNA Seq., 3, 311-318.
63. Maskell, D.J., Szabo, M.J., Deadman, M.E. and Moxon, E.R. (1992) Mol. Microbiol., 6, 3051-3063.
64. Plateau, P., Fromant, M., Schmitter, J.M., Buhler, J.M. and Blanquet, S. (1989) J. Bacteriol., 171, 6437-6445.
65. Koonin, E.V., Altschul, S.F. and Bork, P. (1996) Nature Genet., 13, 266-268.
66. Bork, P., Hofmann, K., Bucher, P., Neuwald, A.F., Altschul, S.F. and Koonin, E.V. (1997) FASEB J., 11, 68-76.
67. Callebaut, I. and Mornon, J.-P. (1997) FEBS Lett., 400, 25-30.
68. Miki, Y., Swensen, J., Shattuck-Eidens, D., Futreal, P.A., Harshman, K., Tavtigian, S., Liu, Q., Cochran, C., Bennett, L.M., Ding, W., et al. (1994) Science, 266, 66-71.
69. Wu, L.C., Wang, Z.W., Tsan, J.T., Spillman, M.A., Phung, A., Xu, X.L., Yang, M.C., Hwang, L.Y., Bowcock, A.M. and Baer, R. (1996) Nature Genet., 14, 430-440.
70. Tanaka, T. and Tanaka, M. (1996) DDBJ accession no. D87228.
71. 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.
72. Johnson, A.F., de la Bastide, M., Lodhi, M., Hoffman, J., Hasegawa, A., Gnoj, L., Gottesman, T., Granat, S., Hameed, A., Kaplan, N., et al. (1997) GenBank accession no. 2104545.
73. Nagase, T., Seki, N., Ishikawa, K., Ohira, M., Kawarabayasi, Y, Ohara, O., Tanaka, A., Kotani, H., Miyajima, N. and Nomura, N. (1996) DNA Res., 3, 321-329.
74. 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.
75. Barrell, B.G., Rajandream, M.A. and Connor, R.E. (1996) EMBL accession no. Z81317.
76. Johnston, M., Andrews, S., Brinkman, R., Cooper, J., Ding, H., Du, Z., Favello, A., Fulton, L., Gattung, S., Greco, T., et al. (1994) GenBank accession no. 662142.
77. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M, Sugiura, M., Sasamoto, S., et al. (1996) DNA Res., 3, 109-136.
78. Tabata, S. (1996) GenBank accession no. 1651660.
79. Allende, M.L., Amsterdam, A., Becker, T., Kawakami, K., Gaiano, N. and Hopkins, N. (1996) Genes Dev., 10, 3141-3155.
80. Hernandez, K., Weber, N., Wipfli, P. and Schmidheini, T. (1996) EMBL accession no. Z72888.
81. Sonnhammer, E.L. and Durbin, R. (1994) Comput. Appl. Biosci., 10, 301-307.
82. Gotoh, O. (1982) J. Mol. Biol., 162, 705-708.
83. Fitch, W.M. and Smith, T.F. (1983) Proc. Natl. Acad. Sci. USA, 80, 1382-1386.
84. Altschul, S.F. and Erickson, B.W. (1986) Bull. Math. Biol., 48, 603-616.
85. Myers, E.W. and Miller, W. (1988) Comput. Appl. Biosci., 4, 11-17.
86. Altschul, S.F. Proteins, in press.
87. Richardson, M., Dilworth, M.J. and Scawen, M.D. (1975) FEBS Lett., 51, 33-37.
88. Matsuda, G., Maita, T., Braunitzer, G. and Schrank, B. (1980) Hoppe-Seyler's Z. Physiol. Chem., 361, 1107-1116.
89. Tokunaga, O., Yaegashi, T., Lowe, J., Dobbs, L. and Padmanabhan, R. (1986) Virology, 155, 418-433.
90. Fulton, L. and Waterston, R. (1995) GenBank accession no. 1176713.