A computational gene is a molecular automaton

Automaton

An automaton is a self-operating machine. The word is sometimes used to describe a robot, more specifically an autonomous robot. An alternative spelling, now obsolete, is automation.-Etymology:...

 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

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

, which is used as a
skeleton to encode the input and the transitions of the automaton
(Fig. 1A). The conserved features of a structural gene
(e.g., DNA polymerase

DNA polymerase

A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....

 binding site, start and stop codons, and splicing
sites) 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 (symbols, states,
and transitions) are the design parameters of the computational
gene.