GASCO: Genetic algorithm simulation for codon optimization

In Silico Biology

Volumn 8, Issue 2, 2008, Pages 187-192

  Sandhu, Kuljeet Singh ^a,b   Pandey, Sunil ^a   Maiti, Souvik ^a   Pillai, Beena ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Codon optimization; CpG motif; DNA vaccine; Genetic algorithm

Indexed keywords

ARTICLE; CODON; COMPUTER PROGRAM; CPG ISLAND; DRUG DESIGN; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC ENGINEERING; IMMUNE RESPONSE; SEARCH ENGINE;

ALGORITHMS; BASE SEQUENCE; CODON; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; INTERNET; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 48949116363     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (9)

1. Ramakrishna, L., Anand, K. K., Mohankumar, K. M. and Ranga, U. (2004). Codon optimization of the tat antigen of human immunodeficiency virus type 1 generates strong immune responses in mice following genetic immunization. J. Virol. 78, 9174-9189.
2. Kojima, Y., Xin, K. Q., Ooki, T., Hamajima, K., Oikawa, T., Shinoda, K., Ozaki, T., Hoshino, Y., Jounai, N., Nakazawa, M., Klinman, D. and Okuda, K. (2002). Adjuvant effect of multi-CpG motifs on an HIV-1 DNA vaccine. Vaccine 20, 2857-2865.
3. Zhang, A., Jin, H., Zhang, F., Ma, Z., Tu, Y., Ren, Z., Zhang, X., Zhu, K. and Wang, B. (2005). Effects of multiple copies of CpG on DNA vaccination. DNA Cell Biol. 24, 292-298.
4. Van Uden, J. and Raz, E. (1999). Immunostimulatory DNA and applications to allergic disease. J. Allergy Clin. Immunol. 104, 902-910.
5. Fuglsang, A. (2003). Codon optimizer: A freeware tool for codon optimization. Protein Expr. Purif. 31, 247-249.
6. Gao, W., Rzewski, A., Sun, H., Robbins, R D. and Gambotto, A. (2004). UpGene: Application of a web-based DNA codon optimization algorithm. Biotechnol. Prog. 20, 443-448.
7. Harish, N., Gupta, R., Agarwal, P., Scaria, V. and Pillai, B. (2006). DyNAVacS: An integrative tool for optimized DNA vaccine design. Nucleic Acids Res. 34, W264-W266.
8. Satya, R. V., Mukherji, M. and Ranga, U. (2003). A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression Vectors. In: Proceedings of Computational System Bioinformatics (CSB'03), IEEE, pp. 294-305.
9. Krieg, A. M., Wu, T., Weeratna, R., Efier, S. M., Love-Homan, L., Yang, L., Yi, A.-K., Short, D. and Davis, H. L. (1998). Sequence motifs in adenoviral DNA block immune activation by stimulatory CpG motifs. Proc. Natl. Acad. Sci. USA 95, 12631-12636.