Optimizing the codon usage of synthetic gene with QPSO algorithm

Journal of Theoretical Biology

Volumn 254, Issue 1, 2008, Pages 123-127

  Cai, Yujie ^a   Sun, Jun ^a   Wang, Jie ^a   Ding, Yanrui ^a   Tian, Na ^a   Liao, Xiangru ^a   Xu, Wenbo ^a  

^a JIANGNAN UNIVERSITY   (China)

Author keywords

Codon usage; Quantum behaved Particle Swarm Optimization; Synonymous codon; Synthetic gene

Indexed keywords

SYNTHETIC DNA;

GENE EXPRESSION; GENETIC ALGORITHM; OPTIMIZATION;

ALGORITHM; ARTICLE; CODON; COMPUTER PROGRAM; DNA SEQUENCE; METHODOLOGY; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTUM BEHAVED PARTICLE SWARM OPTIMIZATION; RESTRICTION SITE; RNA SEQUENCE;

ALGORITHMS; CODON; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENES, SYNTHETIC; HUMANS; MODELS, GENETIC;

ANIMALIA;

EID: 49049117997     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.05.010     Document Type: Article

References (28)

1. Akashi H. Synonymous codon usage in Drosophila melanogaster, natural selection and translational accuracy. Genetics 136 (1994) 927-935
2. Alff-Steinberger C. A comparative study of mutations in Escherichia coli and Salmonella typhimurium shows that codon conservation is strongly correlated with codon usage. J. Theor. Biol. 206 (2000) 307-311 10.1006/jtbi.2000.2126
3. Back T., Fogel D., and Michalewicz Z. Handbook of Evolutionary Computation (1997), Oxford University Press, New York
4. Bergh, F.V.D., 2001. An analysis of particle swarm optimizers. Ph.D. Thesis, Department of Computer Science, University of Pretoria, Pretoria, South Africa.
5. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 129 (1991) 897-907
6. Chechetkin V.R. Genetic code from tRNA point of view. J. Theror. Biol. 242 (2006) 922-934 10.1016/j.jtbi.2006.05.008
7. Clerc M., and Kennedy J. The particle swarm: explosion, stability and convergence in a multi-dimensional complex space. IEEE Trans. Evolut. Comput. 6 (2002) 58-73
8. Fuglsang A. Codon optimizer: a freeware tool for codon optimization. Protein Expres. Purif. 31 (2003) 247-249 10.1016/S1046-5928(03)00213-4
9. Grantham R., Gautier C., Gouy M., Mercier R., and Pave R. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8 (1980) 49-62
10. Grote A., Hiller K., Scheer M., Munch R., Nortemann B., Hempel D.C., and Jahn D. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 33 Web Server issue (2005) W526-W531
11. Hamed S.N., Hani G., and Noorossadat T. Optimality of codon usage in Escherichia coli due to load minimization. J. Theror. Biol. 237 (2005) 203-209 10.1016/j.jtbi.2005.04.007
12. Hoover D.M., and Lubkowski J. DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res. 30 (2002) e43
13. Jayaraj S., Reid R., and Santi D.V. GeMS: an advanced software package for designing synthetic genes. Nucleic Acids Res. 33 (2005) 3011-3016
14. Kennedy, J., Eberhart, R., 1995. Particle swarm optimization, Proceedings of the IEEE International Conference on Neural Network 1942-1948.
15. Pesole G., Attimonelli M., and Liuni S. A backtranslation method based on codon usage strategy. Nucleic Acids Res. 16 (1988) 1715-1728
16. Puigbò P., Guzmán E., Romeu A., and Garcia-Vallvé S. OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res. 35 Web Server issue (2007) 1-6
17. Richardson S.M., Wheelan S.J., Yarrington R.M., and Boeke J.D. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res. 16 (2006) 550-556
18. Sharp P.M., Stenico M., Peden J.F., and Lloyd A.T. Codon usage: mutational bias, translational selection, or both?. Biochem. Soc. Trans. 21 (1993) 835-841
19. Sharp P.M., Averof M., Lloyd A.T., Matassi G., and Peden J.F. DNA sequence evolution: the sounds of silence. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 349 (1995) 241-247
20. Solis F., and Wets R. Minimization by random search techniques. Math Oper. Res. 6 (1981) 19-30
21. Sun, J., Feng, B., Xu, W.B., 2004a. Particle Swarm Optimization with Particles Having Quantum Behavior. In: Proceedings of the 2004 Congress on Evolutionary Computation, Piscataway, NJ, pp. 325-331.
22. Sun, J., Feng, B., Xu, W.B., 2004b. A Global Search Strategy of Quantum-behaved Particle Swarm Optimization. In: Proceedings of the 2004 IEEE Conference on Cybernetics and Intelligent Systems, Singapore, pp. 111-115.
23. Sun, J., Feng, B., Xu, W.B., 2005. Adaptive Parameter Control for Quantum-behaved Particle Swarm Optimization on Individual Level. In: Proceedings of the 2005 IEEE International Conference on Systems, Man and Cybernetics. Piscataway, NJ, pp. 3049-3054.
24. Villalobos A., Ness J.E., Gustafsson C., Minshull J., and Govindarajan S. Gene designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinform. 7 (2006) 285
25. Wang G., and Dunbrack R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
26. Weaver R.F. Molecular Biology (2001), McGraw-Hill Science, New York pp. 63-93
27. Willenbrock H., Friis C., Juncke A.S.R., and Ussery D.W. An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol. 7 (2006) R114
28. Wu G., Bashir-Bello N., and Freeland S.J. The synthetic gene designer: a flexible web platform to explore sequence manipulation for heterologous expression. Protein Exp. Purif. 47 (2006) 441-445 10.1016/j.pep.2005.10.020