Enhanced A* algorithms for multiple alignments: Optimal alignments for several sequences and k-opt approximate alignments for large cases

Theoretical Computer Science

Volumn 210, Issue 2, 1999, Pages 341-374

  Ikeda, Takahiro ^a   Imai, Hiroshi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

A Algorithm; A* Algorithm; Group Alignment; Multiple Alignment

Indexed keywords

EID: 0001650390     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0304-3975(98)00093-0     Document Type: Article

References (20)

1. S. Araki, M. Goshima, S. Mon, H. Nakashima, S. Tomita, Y. Akiyama, and M. Kanehisa, Application of parallelized DP and A* algorithm to multiple sequence alignment, Proc. Genome Informatics Workshop IV, 1993, pp. 94-102.
2. M.P. Berger, P.J. Munson, A novel randomized iterative strategy for aligning multiple protein sequences, Comput. Appl. Biosci. 7 (1991) 479-484.
3. H. Carrillo, D.J. Lipman, The multiple sequence alignment problem in biology, SIAM J. Appl. Math. 48 (1988) 1073-1082.
4. M.O. Dayhoff, R.M. Schwartz, B.C. Orcutt, Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, DC, 1978.
5. O. Gotoh, Optimal alignment between groups of sequences and its application to multiple sequence alignment, Comput Appl. Biosci. 9 (1993) 361-370.
6. S.K. Gupta, J.D. Kececioglu, A.A. Schaffer, Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment, J. Comput. Biol. 2 (3) (1995) 459-472.
7. P.E. Hart, N.J. Nillson, B. Rafael, A formal basis for the heuristic determination of minimum cost paths, IEEE Trans. Systems Sci. and Cybernet SSC-4 (1968) 100-107.
8. M. Hirosawa, M. Hoshida, M. Ishikawa, T. Toya, MASCOT: multiple alignment system for protein sequence based on three-way dynamic programming, Comput. Appl. Biosci. 9 (1993) 161-167.
9. M. Hirosawa, Y. Totoki, M. Hoshida, M. Ishikawa, Comprehensive study on iterative algorithms of multiple sequence alignment, Comput. Appl. Biosci. 11 (1) (1995) 13-18.
10. T. Ikeda, Applications of the A* algorithm to better routes finding and multiple sequence alignment, Master's Thesis, Department of Information Science, University of Tokyo, 1995. Available at http://naomi.is.s.u-tokyo.ac.jp/.
11. T. Ikeda, H. Imai: Fast A* Algorithms for multiple sequence alignment, Proc. Genome Informatics Workshop, 1994, pp. 90-99.
12. T. Ikeda, M. Hsu, H. Imai, S. Nishimura, H. Shimoura, T. Hashimoto, K. Temmoku, K. Mitoh, A fast algorithm for finding better routes by AI search techniques, Proc. Internat. Conf. on Vehicle Navigation & Information Systems (VNIS'94), 1994, pp. 291-296.
13. H. Imai, T. Ikeda, k-Group multiple alignment based on A* search, Proc. Genome Informatics Workshop, Yokohama, 1995, pp. 9-18.
14. G. Shibayama, H. Imai, Finding K-best alignment of multiple sequences, Proc. Genome Informatics Workshop IV, 1993, pp. 120-129.
15. T. Shibuya, H. Imai, Enumerating suboptimal alignments of multiple biological sequences efficiently, Proc. Pacific Symp. on Biocomputing, 1997, pp. 409-420.
16. T. Shibuya, H. Imai, Parametric alignment of multiple biological sequences, Proc. Genome Informatics Workshop, 1996, pp. 41-50.
17. T. Shibuya, H. Imai, New Flexible approaches for multiple sequence alignment, J. Comput. Biol. 4 (3) (1997) pp. 385-413; a preliminary version was presented at Proc. 1st ACM Ann. Internat. Conf. on Computational Molecular Biology, 1997, pp. 267-276.
18. T. Shibuya, H. Imai, New Flexible approaches for multiple sequence alignment, J. Comput. Biol. 4 (3) (1997) pp. 385-413; a preliminary version was presented at Proc. 1st ACM Ann. Internat. Conf. on Computational Molecular Biology, 1997, pp. 267-276.
19. J.L. Spouge, Speeding up dynamic programming algorithms for finding optimal lattice paths, SIAM J. Appl. Math. 49 (1989) 1552-1566.
20. M.S. Waterman, Introduction to Computational Biology: Maps, Sequences and Genomes, Chapman & Hall, London, 1995.