GASCO

Genetic Algorithm Simulation for Codon Optimisation   

Codon optimization is a generic technique to achieve optimum expression of a foreign gene in the host’s cell system. Selection of optimum codons depends on codon usage of the host genome and the presence of several desirable and undesirable sequence motifs. Searching these motifs in all possible combinations of the codons increases the search space exponentially with respect to sequence length. GASCO is an algorithm developed for the optimum codon selection using genetic algorithms. The algorithm reduces the search space and provides an approximate solution to the problem. The algorithm has applications in DNA vaccine design for successfully eliciting potent immune responses.

Software Requirements


PERL 5.8 or later with following libraries installed-

1.  Tk (Toolkit): Available by default except few like Tk::Graph that can be downloaded either

    from CPAN or ASPNPerl (Programmer’s package manager)

2.  LWP, HTTP and HTML: available by default.

Download windows setup
Download source-code
Download user-manual


 

For queries and comments write to kuljeets@igib.res.in  or kulsandhu@rediffmail.com

Authors: Kuljeet Singh Sandhu, Sunil Pandey, Souvik Maiti and Beena Pillai

G.N Ramachandran Knowledge Center for Genome Informatics,
Institute of Genomics and Integrative Biology
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