RAGA: RNA sequence alignment by genetic algorithm

Nucleic Acids Research

Volumn 25, Issue 22, 1997, Pages 4570-4580

  Notredame, Cédric ^a   O'Brien, Emmet A ^a,b   Higgins, Desmond G ^a,b  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENETIC PROCEDURES; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE;

EID: 0030813152     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.22.4570     Document Type: Article

References (40)

1. Needleman,S.B. and Wunsch,C.D. (1970) J. Mol. Bio., 48, 443-453.
2. Michot,B., Qu,L.H. and Bachellerie,J.P. (1990) Eur. J. Biochem., 188, 219-229.
3. Gutell,R.R., Weiser,B., Woese,C.R. and Noller,H.F. (1985) Prog. Nucleic Acid Res. Mol. Biol., 32, 155-216.
4. Zuker,M. (1989) Science, 244, 48-52.
5. Gouy,M. (1987) In Bishop,M.J. and Rawlings,C.J. (eds). Nucleic Acid and Protein Sequence Analysis: A Practical Approach. IRL Press, Oxford, UK, pp. 259-284.
6. Schmitz,M. and Steger,G. (1996) J. Mol. Biol., 255, 254-266.
7. Shapiro,B.A. and Wu,J.C. (1996) Comput. Applicat. Biosci., 12, 171-180.
8. Gultayaev,A.P., van Batenburg,F.D.H. and Pleij,C.W.A. (1995) J. Mol. Biol., 250, 37-51.
9. Ogata,H., Yutaka,A. and Minoru,K. (1995) Nucleic Acids Res., 23, 419-426.
10. Sankoff,D. (1985) SIAM J. Applicat. Math., 45, 810-825.
11. Eddy,S.R. and Durbin,R. (1994) Nucleic Acids Res., 22, 2079-2088.
12. Kim,J., Cole,J.R. and Pramanik,S. (1996) Comput. Applicat. Biosci., 12, 259-267.
13. Lathrop,R.H. (1994) Protein Engng, 7, 1059-1068.
14. Sakakibara,Y., Brown,M., Underwood,R.C., Mian,I.S. and Haussler,D. (1994) In 27th Hawaii International Conference on System Sciences. IEEE Computer Society Press, Los Alamitos, CA, pp. 284-293.
15. Lefebvre,F. (1995) In ISMB-95. AAAI Press, CA, pp. 222-230.
16. Pleij,C. (1990) Trends Biochem. Sci., 15, 143-147.
17. Tabaska,E.J. and Stormo,G.S. (1997) In ISMB-97. AAAI Press, Menlo Park, CA, pp. 311-318.
18. Corpet, F. and Michot,B. (1994) Comput. Applicat. Biosci., 10, 389-99.
19. Davis,L. (1991) The Handbook of Genetic Algorithms. Van Nostrand Reinhold, New York, NY.
20. Goldberg,D.E. (1989) Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley, New York, NY.
21. Kirkpatrick,S., Gelatt,C.D.J. and Vecchi,M.P (1983) Science, 220, 671-680.
22. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Science, 262, 208-214.
23. Notredame,C. and Higgins,D.G. (1996) Nucleic Acids Res., 24, 1515-1524.
24. Thompson,J.D. (1995) Comput. Applicat. Biosci., 11, 19-29.
25. Thompson,J., Higgins,D. and Gibson,T. (1994) Nucleic Acids Res., 22, 4673-4690.
26. Gerstein,M. and Levitt,M. (1996) In Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 59-67.
27. Gotoh,O. (1993) Comput. Applicat. Biosci., 9, 361-370.
28. Myers,E.W. and Miller,W. (1988) Comput. Applicat. Biosci., 4, 11-17.
29. Van de Peer,Y., Jansen J., De Rijk,P. and De Watcher,R. (1997) Nucleic Acids Res., 25, 111-116.
30. Neefs,J.M. and De Wachter,R. (1990) Nucleic Acids Res., 18, 5695-5704.
31. Neefs,J.M., Van de Peer,Y., De Rijk,P., Chapelle,S. and De Wachter,R. (1993) Nucleic Acids Res., 21, 3025-3049.
32. Subramanian,A.R. (1985) Essays Biochem., 21, 45-85.
33. Felsenstein,J. (1988) Cladistics, 5, 355-356.
34. Kimura,M. (1980) J. Mol. Evol., 16, 111-120.
35. Gotoh,O. (1982) J. Mol. Biol. 162, 705-708.
36. Gotoh,O (1990) Bull. Math. Bio., 52, 509-525.
37. Westhof,E. and Jaeger,L. (1992) Curr. Opin. Struct. Biol., 2, 327-333.
38. Abrahams,J.P., van der Berg,M., van Batenburg,E. and Pleij,C. (1990) Nucleic Acids Res., 18, 3035-3044.
39. Grate,L. (1995) In ISMB-95. AAAI Press, Menlo Park, CA, pp. 136-144.
40. Shapiro,B.A., Maizel,J., Lipkin,L.E., Currey,K. and Whitney,C (1984) Nucleic Acids Res., 12, 75-88.