Question: Extract the optimized DNA sequence from a GeneGA instance
gravatar for tomas.bjorklund
2.5 years ago by
tomas.bjorklund20 wrote:

I'm using the GeneGA package to optimize the codon utilization and secondary structure of a large list of DNA sequences. The program works as expected, but I have issues figuring out the GeneGA instance generated and the documentation is very sparse.... if I pipe the output of GeneGA to a GeneGA.results object, I can show the optimal sequence using the show(GeneGA.results) together with two other iterations and their free energy. However, I cannot figure out how to extract only the optimized DNA sequence for further analysis. Using GeneGA.results@seq I can see the original input sequence, but that is not all that useful.... I would need something similar for the optimal sequence and that appears not to be available.

I apologize if this is obvious, but I'm still learning R... 


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