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A computational gene is a molecular automaton consisting of a structural part and a functional part; and its design is such that it might work in a cellular environment.
The structural part is a naturally occurring gene, which is used as a skeleton to encode the input and the transitions of the automaton. The conserved features of a structural gene serve as constants of the computational gene, while the coding regions, the number of exons and introns, the position of start and stop codon, and the automata theoretical variables are the design parameters of the computational gene. The constants and the design parameters are linked by several logical and biochemical constraints. The input of the automaton are molecular markers given by single stranded DNA molecules. These markers are signalling aberrant molecular phenotype and turn on the self-assembly of the functional gene. If the input is accepted, the output encodes a double stranded DNA molecule, a functional gene which should be successfully integrated into the cellular transcription and translation machinery producing a wild type protein or an anti-drug. Otherwise, a rejected input will assemble into a partially dsDNA molecule which cannot be translated.