Improvement of clustal-derived sequence alignments with evolutionary algorithms

2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings

Volumn 1, Issue , 2003, Pages 312-319

  Thomsen, René ^a   Fogel, Gary B ^b   Krink, Thiemo ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b NATURAL SELECTION INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARKING; BIOINFORMATICS; CALCULATIONS;

CENTRAL PROBLEMS; EVOLUTIONARY ALGORITHMS (EAS); INITIAL POPULATION; MULTIPLE SEQUENCE ALIGNMENTS; PROTEIN SEQUENCE ALIGNMENTS; SEQUENCE ALIGNMENTS; SUBSTITUTION MATRIX; SUM-OF-PAIRS SCORE;

EVOLUTIONARY ALGORITHMS;

EID: 84901398952     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2003.1299591     Document Type: Conference Paper

References (14)

1. L. Cai, D. Juedes. and E. Liakhovitch. Evolutionary computation techniques for multiple sequence alignment. In A. Zalzala, C. Fonseca, J.-H. Kim, and A. Smith, editors, Proceedings of the Second Congress on Evolutionary Computation (CEC-2000), pp. 829-835, 2000.
2. K. Chellapilla and G. B. Fogel. Multiple sequence alignment using evolutionary programming. In P. J. Angeline, Z. Michalewicz, M. Schoenauer, X. Yao. and A. Zalzala, editors. Proceedings of the First Congress of Evolutionary Computation (CEC-1999), pp. 445-452, 1999.
3. D. F. Feng and R. F. Doolittle. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Ewtl. Vol. 25, No. 4, pp. 351-360, 1987.
4. S. K. Gupta, J. D J. D. Kececioglu, and A. A. Schaffer. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J. Comp. Bio., Vol. 2, No. 3, pp. 459-472, 1995.
5. S. Henikoff and. J. G. Henikoff: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. Vol. 89, pp. 10915-10919, 1992.
6. M. Ishikawa, T. Toya, Y. Totoki. and A. Konagaya. Parallel iterative aligner with genetic algorithm. In T. Takagi, H. Imai, S, Miyano, S. Mitaku, and M. Kanehisa, editors, Proceedings of Genome Informatics Workshop IV, pp. 13-22, 1993.
7. J. Kim, S. Pramanik, and M. J. Chung. Multiple sequence alignment using simulated annealing. Computer Applications in the Biosciences (CABlOS), Vol. 10, No. 4, pp. 419-426. 1994.
8. C. Notredame and D. G. Higgins. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Research, Vol. 24, No. 8, pp. 1515-1524, 1996.
9. J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins: The ClustalX windows interface: flexible strategies'for multiple sequence alignment aided by quality analysis tools: Nucleic Acids Research, Vol. 24, pp. 4876-4882', 1997.
10. J. D. Thompson, D. G. Higgins, and T. J. Gibson. Clustal W: improving the' sensitivity of progressive multiple sequence alignment through sequence weighting. Nucleic Acids-Research, Vol. 22, No. 22, pp. 4673-4680. 1994.
11. J. D. Thompson, F. Plewniak, and O. Poch. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, Vol. 15, pp. 87-88, 1999.
12. R. Thomsen, G. B. Fogel, and T. Krink. A alignment improver using evolutionary algorithms. In D. B. Fogel, X. Yao, G. Greenwood, H. Iba. P. Marrow, and M. Shackleton, editors, Proceedings of the Fourth Congress on Evolutionan Computation (CEC-2002). Vol. 1, pp. 121-126, 2002.
13. R. Thomsen and T. Krink, Self-adaptive operator, scheduling using the religion-based EA. In Proceedings of Parallel Problem Solving from Nature. VII (PPSN-2002), pp. 214-223. Springer Verlag, 2002.
14. L. Wang and T. Jiang. On the complexity of multiple sequence alignment. Journal of Computational Biology, Vol. I. No. 4, pp. 337-348. 1994.