Multiple sequence alignment: Algorithms and applications

Advances in Biophysics

Volumn 36, Issue , 1999, Pages 159-206

  Gotoh, Osamu ^a  

^a SAITAMA CANCER CENTER   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; EVOLUTION; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC PROCEDURES; MOLECULAR BIOLOGY; PHYLOGENY; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; RNA ANALYSIS; SEQUENCE ANALYSIS; STOCHASTIC MODEL;

EID: 0032789448     PISSN: 0065227X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-227X(99)80007-0     Document Type: Article

References (189)

1. M. Kimura, "The Neutral Theory of Molecular Evolution," Cambridge University Press, Cambridge (1983).
2. D. Sankoff and J. B. Kruskal, "Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison," Addison-Wesley, New York (1983).
3. M. S. Waterman, "Introduction to Computational Biology," Chapman & Hall, London (1995).
4. R. F. Doolittle (ed.), "Methods in Enzymology," Vol. 183 (1990).
5. R. F. Doolittle (ed.), "Methods in Enzymology," Vol. 266 (1996).
6. M. J. E. Sternberg (ed.), "Protein Structure Prediction," Oxford University Press, Oxford (1996).
7. M. J. Bishop and C. J. Rawlings (eds.), "DNA and Protein Sequence Analysis," Oxford University Press, Oxford (1997).
8. D. Gusfield, "Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology," Cambridge University Press, Cambridge (1997).
9. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids," Cambridge University Press, Cambridge (1998).
10. M. Dayhoff (ed.), "Atlas of Protein Sequence and Structure," Vol. 5, Suppl. 3, National Biomedical Research Foundation, Washington, D.C. (1978).
11. K. Tomii and M. Kanehisa, Protein Eng., 9, 27 (1996).
12. G. H. Gonnet, M. A. Cohen, and S. A. Benner, Science, 256, 1443 (1992).
13. G. Vogt, T. Etzold, and P. Argos, J. Mol. Biol., 249, 816 (1995).
14. O. Gotoh. J. Mol. Biol., 264, 823 (1996).
15. S. Pascarella and P. Argos, J. Mol. Biol., 224, 461 (1992).
16. E. G. Shpaer, M. Robinson, D. Yee, J. D. Candlin, R. Mines, and T. Hunkapiller, Genomics, 38, 179 (1996).
17. S. A. Benner, M. A. Cohen, and G. H. Gonnet, J. Mol. Biol., 229, 1065 (1993). •
18. M. S. Waterman, Bull. Math. Biol., 46, 473 (1984).
19. S. B. Needleman and C. D. Wunsch, J. Mol. Biol., 48, 443 (1970).
20. P. H. Sellers, J. Algorithms, 1, 359 (1980).
21. M. S. Waterman, T. F. Smith, and W. A. Beyer, Adv. Math., 20, 367 (1976).
22. T. F. Smith, M. S. Waterman, and W. M. Fitch, J. Mol. Evol., 18, 38 (1981).
23. D. Sankoff, Proc. Natl. Acad. Sci. USA, 69, 4 (1972).
24. P. H. Sellers, SIAM J. Appl. Math., 26, 787 (1974).
25. R. A. Wagner and M. J. Fischer, J. Assoc. Comp. Mach., 21, 168 (1974).
26. O. Gotoh, J. Mol. Biol., 162, 705 (1982).
27. O. Gotoh, Bull. Math. Biol., 52, 359 (1990).
28. X. Huang, Comput. Appl. Biosci., 10, 227 (1994).
29. W. Miller and E. W. Myers, Bull. Math. Biol., 50, 97 (1988).
30. Z. Galil and R. Giancarlo, Theor. Comp. Sci., 64, 107 (1989).
31. L. Allison, C. S. Wallace, and C. N. Yee, J. Mol. Evol., 35, 77 (1992).
32. A. V. Aho, J. E. Hopcroft, and J. D. Ullman, "Data Structures and Algorithms," Addison-Wesley, Reading (1983).
33. S. F. Altschul and B. W. Erickson, Bull. Math. Biol., 48, 603 (1986).
34. P. Taylor, Nucl. Acids Res., 12, 447 (1984).
35. D. S. Hirshberg, Commun. Assoc. Comput. Mach., 18, 341 (1975).
36. E. W. Myers and W. Miller, Comp. Appl. Biosci., 4, 11 (1988).
37. K.-M. Chao, R. C. Hardison, and W. Miller, J. Comput. Biol., 1, 271 (1994).
38. M. Zuker, J. Mol. Biol., 221, 403 (1991).
39. O. Gotoh, Comp. Appl. Biosci., 9, 361 (1993).
40. O. Gotoh, Comp. Appl. Biosci., 10, 379 (1994).
41. M. Gribskov, A. D. McLachlan, and D. Eisenberg, Proc. Natl. Acad. Sci. USA, 84, 4355 (1987).
42. D. Sankoff, SIAM J. Appl. Math., 78, 35 (1975).
43. S. F. Altschul, J. Theor. Biol., 138, 297 (1989).
44. M. L. Fredman, Bull. Math. Biol., 46, 553 (1984).
45. M. Murata, J. S. Richardson, and J. L. Sussman, Proc. Natl. Acad. Sci. USA, 82, 3073 (1985).
46. O. Gotoh, J. Theor. Biol., 121, 327 (1986).
47. D. Sankoff, R. J. Cedergren, and G. Lapalme, J. Mol. Evol., 7, 133 (1976).
48. H. Imai and T. Ikeda, "Genome Informatics Workshop," Vol. 6, ed. by M. Hagiya et al., Universal Academy, Tokyo, p. 9 (1995).
49. J. W. Fickett, Nucl. Acids Res., 12, 175 (1984).
50. E. Ukkonen, Inf. Control., 64, 100 (1985).
51. H. Carrillo and D. Lipman, SIAM J. Appl. Math., 48, 1073 (1988).
52. J. L. Spouge, SIAM J. Appl. Math., 49, 1552 (1989).
53. J. L. Spouge, Compt. Appl. Biosci., 7, 1 (1991).
54. P.E. Hart, N. J. Nilsson, and B. Raphael, IEEE Trans. Syst. Sci. Cybern., 4, 100 (1968).
55. S. Araki, M. Goshima, S.-i. Mori et al., "Genome Informatics Workshop," Vol. 4, ed. by T. Takagi et al., Universal Academy, Yokohama, p. 94 (1993).
56. D. J. Lipman, S. F. Altschul, and J. D. Kececioglu, Proc. Natl. Acad. Sci. USA, 86, 4412 (1989).
57. S. K. Gupta, J. D. Kececioglu, and A. A. Schaffer, J. Comput. Biol., 2, 459 (1995).
58. T. Ikeda and H. Imai, Theor. Comput. Sci., 210, 341 (1999).
59. H. Kobayashi and H. Imai, "Genome Informatics," Vol. 9, ed. by S. Miyano and T. Takagi, Universal Academy, Tokyo, p. 120 (1998).
60. E. Sobel and H. M. Martinez, Nucl. Acids Res., 14, 363 (1986).
61. L. J. Korn, C. L. Queen, and M. N. Wegman, Proc. Natl. Acad. Sci. USA, 74, 4401 (1977).
62. M. Santibánez and K. Rohde, Comp. Appl. Biosci., 3, 111 (1987).
63. M. Vingron and P. Argos, Comp. Appl. Biosci., 5, 115 (1989).
64. J.-P. Dumas and J. Ninio, Nucl. Acids Res., 10, 197 (1982).
65. W. J. Wilbur and D. J. Lipman, Proc. Natl. Acad. Sci. USA, 80, 726 (1983).
66. G. D. Schuler, S. F. Altschul, and D. J. Lipman, Proteins, 9, 180 (1991).
67. R. Staden, Nucl. Acids Res., 10, 2951 (1982).
68. M. Vingron and P. Argos, J. Mol. Biol., 218, 33 (1991).
69. M. Vingron and P. A. Pevzner, Adv. Appl. Math., 16, 1 (1995).
70. E. Depiereux and E. Feytmans, Comp. Appl. Biosci., 8, 501 (1992).
71. B. Morgenstern, A. Dress, and T. Werner, Proc. Natl. Acad. Sci. USA, 93, 12098 (1996).
72. M. S. Johnson and R. F. Doolittle, J. Mol. Evol., 23, 267 (1986).
73. M. S. Waterman, Nucl. Acids Res., 14, 9095 (1986).
74. O. Gotoh, Bull. Math. Biol., 52, 509 (1990).
75. W. Miller, Comput. Appl. Biosci., 9, 169 (1993).
76. M. Vingron and P. Argos, Protein Eng., 3, 565 (1990).
77. K.-M. Chao, R. C. Hardison, and W. Miller, Comput. Appl. Biosci., 9, 387 (1993).
78. H. T. Mevissen and M. Vingron, Protein Eng., 9, 127 (1996).
79. M. J. Bishop and E. A. Thompson, J. Mol. Biol., 190, 159 (1986).
80. J. L. Thorne, H. Kishino, and J. Felsenstein, J. Mol. Evol., 33, 114 (1991).
81. J. L. Thorne, H. Kishino, and J. Felsenstein, J. Mol. Evol., 34, 3 (1992).
82. M. Q. Zhang and T. G. Marr, J. Theor. Biol., 174, 119 (1995).
83. S. Miyazawa, Protein Eng., 8, 999 (1995).
84. U. Tönges, S. W. Perrey, J. Stoye, and A. W. M. Dress, Gene, 172, GC33 (1996).
85. G. Brinkmann, A. W. M. Dress, S.W. Perrey, and J. Stoye, "Mathematical Programming," Vol. 79, ed. by T. M. Liebling and D. de Werra, Elsevier, Amsterdam, p. 71 (1997).
86. J. Stoye, Gene, 211, GC45 (1998).
87. P. Hogeweg and B. Hesper, J. Mol. Evol., 20, 175 (1984).
88. M. S. Waterman and M. D. Perlwitz, Bull. Math. Biol., 46, 567 (1984).
89. D.-F. Feng and R. F. Doolittle, J. Mol. Evol., 25, 351 (1987).
90. W. R. Taylor, J. Mol. Evol., 28, 161 (1988).
91. G. J. Barton and M. J. E. Sternberg, J. Mol. Biol., 198, 327 (1987).
92. R. F. Smith and T. F. Smith, Proc. Natl. Acad. Sci. USA, 87, 118 (1990).
93. F. Corpet, Nucl. Acids Res., 16, 10881 (1988).
94. D. G. Higgins and P. M. Sharp, Comp. Appl. Biosci., 5, 151 (1989).
95. J. Hein, Mol. Biol. Evol., 6, 649 (1989).
96. S. C. Chan, A. K. C. Wong, and D. K. Y. Chiu, Bull. Math. Biol., 54, 563 (1992).
97. D.-F. Feng and R. F. Doolittle, Methods Enzymol., 266, 368 (1996).
98. D. G. Higgins, J. D. Thompson, and T. J. Gibson, Methods Enzymol., 266, 383 (1996).
99. J. Hein, Mol. Biol. Evol., 6, 669 (1989).
100. O. Trelles, M. A. Andrade, A. Valencia, E. L. Zapata, and J. M. Carazo, Bioinformatics, 14, 439 (1998).
101. W. Bains, Nucl. Acids Res., 14, 159 (1986).
102. J. D. Thompson, D. G. Higgins, and T. J. Gibson, Nucl. Acids Res., 22, 4673 (1994).
103. W. R. Taylor, Gene, 1, GC27 (1995).
104. A. Krogh, M. Brown, I. S. Mian, K. Sjölander, and D. Haussler, J. Mol. Biol., 235, 1501 (1994).
105. P. Baldi, Y. Chauvin, T. Hunkapiller, and M. A. McClure, Proc. Natl. Acad. Sci. USA, 91, 1059 (1994).
106. L. R. Rabiner, Proc. IEEE, 77, 257 (1989).
107. R. Hughey and A. Krogh, Comput. Appl. Biosci., 12, 95 (1996).
108. S. Subbiah and S. C. Harrison, J. Mol. Biol., 209, 539 (1989).
109. M. P. Berger and P. J. Munson, Comp. Appl. Biosci., 7, 479 (1991).
110. M. Hirosawa, Y. Totoki, M. Hoshida, and M. Ishikawa, Comp. Appl. Biosci., 11, 13 (1995).
111. S. F. Altschul, R. J. Carroll, and D. J. Lipman, J. Mol. Biol., 207, 647 (1989).
112. O. Gotoh, Comp. Appl. Biosci., 11, 543 (1995).
113. S. Kirkpatrick, C. D. J. Gelatt, and M. P. Vecchi, Science, 220, 671 (1983).
114. A. V. Lukashin, J. Engelbrecht, and S. Brunak, Nucl. Acids Res., 20, 2511 (1992).
115. M. Ishikawa, T. Toya, M. Hoshida, K. Nitta, A. Ogiwara, and M. Kanehisa, Comput. Appl. Biosci., 9, 267 (1993).
116. J. Kim, S. Pramanik, and M. J. Chung, Comput. Appl. Biosci., 10, 419 (1994).
117. A. Šali and T. L. Blundell, J. Mol. Biol., 212, 403 (1990).
118. L. Holm and C. Sander, J. Mol. Biol., 233, 123 (1993).
119. M. S. Johnson, J. P. Overington, and T. L. Blundell, J. Mol. Biol., 231, 735 (1993).
120. M. Hirosawa, M. Hoshida, M. Ishikawa, and Y. Toya, Comput. Appl. Biosci., 9, 161 (1993).
121. A. Godzik and J. Skolnick, Comput. Appl. Biosci., 10, 587 (1994).
122. D. E. Goldberg, "Genetic Algorithms in Search, Optimization and Machine Learning," Addison-Wesley, New York (1989).
123. K. Tajima, "Genome Informatics Workshop," Vol. 4, ed. by T. Takagi et al., Universal Academy, Yokohama, p. 183 (1993).
124. C. Notredame and D. G. Higgins, Nucl. Acids Res., 24, 1515 (1996).
125. M. Ishikawa, T. Toya, Y. Totoki, and A. Konagaya, "Genome Informatics Workshop," Vol. 4, ed. by T. Takagi et al., Universal Academy, Yokohama, p. 84 (1993).
126. C. Notredame, E. A. O'Brien, and D. G. Higgins, Nucl. Acids Res., 25, 4570 (1997).
127. C. Notredame, L. Holm, and D. G. Higgins, Bioinformatics, 14, 407 (1998).
128. O. Gotoh, "Genome Informatics Workshop," Vol. 4, ed. by T. Takagi et al., Universal Academy, Yokohama, p. 109 (1993).
129. T. F. Smith and M. S. Waterman, J. Mol. Biol., 147, 195 (1981).
130. W. B. Goad and M. I. Kanehisa, Nucl. Acids Res., 10, 247 (1982).
131. O. Gotoh, Comp. Appl. Biosci., 3, 17 (1987).
132. A. Šali and J. P. Overington, Protein Sci., 3, 1582 (1994).
133. A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, J. Mol. Biol., 247, 536 (1995).
134. S. Pascarella, F. Milpetz, and P. Argos, Protein Eng., 9, 249 (1996).
135. L. Holm and C. Sander, Nucl. Acids Res., 24, 206 (1996).
136. K. Mizuguchi, C. M. Deane, T. L. Blundell, and J. P. Overington, Protein Sci., 7, 2469 (1998).
137. R. Sowdhamini, D. F. Burke, J. F. Huang et al., Structure, 6, 1087 (1998).
138. A. Godzik, Protein Sci., 5, 1325 (1996).
139. M. A. McClure, T. K. Vasi, and W. M. Fitch, Mol. Biol. Evol., 11, 571 (1994).
140. P. Briffeuil, G. Baudoux, C. Lambert et al., Bioinformatics, 14, 357 (1998).
141. B. Rost and C. Sander, J. Mol. Biol., 232, 584 (1993).
142. R. King and M. J. E. Sternberg, Protein Sci., 5, 2298 (1996).
143. J. Felsenstein, PHYLIP Ver. 3.5c, University of Washington, Seattle (1992).
144. J. Adachi and M. Hasegawa, MOLPHY Ver. 2.3, Comput. Sci. Monogr., 28, 1 (1996).
145. J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, Nucl. Acids Res., 25, 4876 (1997).
146. L. Brocchieri and S. Karlin, J. Mol. Biol., 276, 249 (1998).
147. J. Felsenstein, Annu. Rev. Genet., 22, 521 (1988).
148. M. Nei, Annu. Rev. Genet., 30, 371 (1996).
149. D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis, "Molecular Systematics," 2nd ed., ed. by D. M. Hillis, C. Moritz, and B. K. Mable, Sunderland, Sinauer, p. 407 (1996).
150. N. Saitou, Methods Enzymol., 266, 427 (1996).
151. M. Hasegawa and H. Kishino, "Bunshi Keitougaku," Iwanami, Tokyo (1996) (in Japanese).
152. D. A. Morrison and J. T. Ellis, Mol. Biol. Evol., 14, 428 (1997).
153. Z. Yang, J. Mol. Evol., 39, 306 (1994).
154. J. A. Lake, Mol. Biol. Evol., 8, 378 (1991).
155. L. Allison and C. S. Wallace, J. Mol. Evol., 39, 418 (1994).
156. G. Mitchison and R. Durbin, J. Mol. Evol., 41, 1139 (1995).
157. P. Bork and E. Koonin, Nature Genet., 18, 313 (1998).
158. T. F. Smith, Trends Genet., 14, 291 (1998).
159. J. Park, K. Karplus, C. Barren et al., J. Mol. Biol., 284, 1201 (1998).
160. T.-M. Yi and E. S. Lander, Protein Sci., 3, 1315 (1994).
161. A. F. Neuwald, J. S. Liu, D. J. Lipman, and C. E. Lawrence, Nucl. Acids Res., 25, 1665 (1997).
162. S. F. Altschul, T. L. Madden, A. A. Schaffer et al., Nucl. Acids Res., 25, 3389 (1997).
163. S. Karlin and S. F. Altschul, Proc. Natl. Acad. Sci. USA, 87, 2264 (1990).
164. S. Karlin and S. F. Altschul, Proc. Natl. Acad. Sci. USA, 90, 5873 (1993).
165. A. L. Hughes and M. Nei, Nature, 335, 167 (1988).
166. O. Gotoh, J. Biol. Chem., 267, 83 (1992).
167. M. A. S. Saqi, P. A. Bates, and M. J. E. Sternberg, Protein Eng., 5, 305 (1992).
168. T. L. Blundell, B. L. Sibanda, M. J. E. Sternberg, and J. M. Thornton, Nature, 326, 347 (1987).
169. A. M. Lesk, M. Levitt, and C. Chothia, Protein Eng., 1, 77 (1986).
170. Z. Y. Zhu, A. Šali, and T. L. Blundell, Protein Eng., 5, 43 (1992).
171. J. M. Levin, S. Pascarella, P. Argos, and J. Garnier, Protein Eng., 6, 849 (1996).
172. B. Rost, C. Sander, and R. Schneider, J. Mol. Biol., 235, 13 (1994).
173. A. A. Salamov and V. V. Solovyev, J. Mol. Biol., 247, 11 (1995).
174. P. K. Mehta, J. Heringa, and P. Argos, Protein Sci., 4, 2517 (1995).
175. N. Goldman, J. L. Thorne, and D. T. Jones, J. Mol. Biol., 263, 196 (1996).
176. F. Fischel-Ghodsian, G. Mathiowitz, and T. F. Smith, Protein Eng., 3, 577 (1990).
177. L. H. Bell, J. R. Coggins, and E. J. Milner-White, Protein Eng., 6, 683 (1993).
178. J.-F. Gibrat, J. Garnier, and B. Robson, J. Mol. Biol., 198, 425 (1987).
179. B. Rost, R. Schneider, and C. Sander, J. Mol. Biol., 270, 471 (1997).
180. H. Peltola, H. Soderlund, and E. Ukkonen, Nucl. Acids Res., 14, 99 (1986).
181. D. J. States and D. Botstein, Proc. Natl. Acad. Sci. USA, 88, 5518 (1991).
182. X. Huang and J. Zhang, Comput. Appl. Biosci., 12, 497 (1996).
183. M. S. Gelfand, A. A. Mironov, and P. A. Pevzner, Proc. Natl. Acad. Sci. USA, 93, 9061 (1996).
184. R. H. Lathrop, Protein Eng., 7, 1059 (1994).
185. J. U. Bowie, R. Lüthy, and D. Eisenberg, Science, 253, 164 (1991).
186. O. Gotoh, Mol. Biol. Evol., 15, 1447 (1998).
187. R. B. Russell and G. J. Barton, Proteins, 14, 309 (1992).
188. W. R. Taylor, T. P. Flores, and C. A. Orengo, Protein Sci., 3, 1858 (1994).
189. W. R. Taylor, J. Mol. Biol., 269, 902 (1997).