AlineaGA: A genetic algorithm for multiple sequence alignment

Studies in Computational Intelligence

Volumn 134, Issue , 2008, Pages 309-318

  da Silva, Fernando José Mateus ^a   Pérez, Juan Manuel ^b   Pulido, Juan Antonio ^b   Rodríguez, Miguel A ^b  

^a POLYTECHNIC INSTITUTE OF LEIRIA   (Portugal)

^b UNIVERSITY OF EXTREMADURA   (Spain)

Author keywords

Bioinformatics; Genetic algorithms; Multiple sequence alignments

Indexed keywords

EID: 45949084831     PISSN: 1860949X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-79355-7_30     Document Type: Article

References (17)

1. Pal, S.K., Bandyopadhyay, S., Ray, S.S.: Evolutionary computation in bioinformatics: A review. IEEE Transactions on Systems Man and Cybernetics Part C-Applications and Reviews 36, 601-615 (2006)
2. Horng, J., Wu, L., Lin, C., Yang, B.: A genetic algorithm for multiple sequence alignment. Soft Computing 9, 407-420 (2005)
3. Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302, 205-217 (2000)
4. Lecompte, O., Thompson, J.D., Plewniak, F., Thierry, J.-C., Poch, O.: Multiple alignment of complete sequences (MACS) in the post-genomic era, Gene, pp. 17-30 (2001)
5. Anbarasu, L.A., Narayanasamy, P., Sundararajan, V.: Multiple molecular sequence alignment by island parallel genetic algorithm. Current Science 78, 858-863 (2000)
6. Holland, J.H.: Adaptation in Natural and Artificial Systems. University of Michigan Press, Ann Arbor (1975)
7. Michalewicz, Z.: Genetic algorithms + data structures = evolution programs - Third, Revised and Extended Edition. Springer, Heidelberg (1996)
8. de Vega, F.F.: Parallel and Distributed Genetic Programming Models with applications to Logic Síntesis on FPGAs. Computer Science Department, vol. PhD., Universidad de Extremadura, Cáceres, p. 156 (2001)
9. De Jong, K.: Learning with genetic algorithms: An overview. Machine Learning 3, 121-138 (1988)
10. Sotredame, C., Higgins, D.G.: SAGA: sequence alignment by genetic algorithm. Nucleic Acids Research 24, 1515-1524 (1996)
11. Notredame, C., O'Brien, E.A., Higgins, D.G.: RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Research 25, 4570-4580 (1997)
12. Nicholas Jr., H.B., Ropelewski, A.J., Deerfield II, D.W.: Strategies for Multiple Sequence Alignment. BioTechniques 32, 572-591 (2002)
13. Wang, C., Lefkowitz, E.J.: Genomic multiple sequence alignments: refinement using a genetic algorithm. BMC Bioinformatics 6 (2005)
14. ThompIon, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680 (1994)
15. L, J.: Calculate PAM Matrix. Wageningen Bioinformatics Webportal (2004), http://www.bioinformatics.nl/tools/pam.html
16. Goldberg, D.E.: Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley Publishing Company, Reading (1989)
17. Zhang, C., Wong, A.K.C.: A genetic algorithm for multiple molecular sequence alignment. Comput. Appl. Biosci. 13, 565-581 (1997)