Gene Expression with General Purpose Graph Rewriting Systems

A Graph Grammar for Modelling RNA Folding

“…Graph transformation can be viewed as an algebraic approach that creates a new graph from a given one by applying rewriting rules [3]. In computational biology graph transformation has been applied in different contexts: Beck et al showed how graph-rewriting algorithms can be employed to model one aspect of whole-organism morphogenesis [2]; the complexity of RNA tertiary structure motifs was encoded by a graph-grammar [15]; and gene expression was simulated using a general purpose graph rewriting system [14]. Generally speaking, graph rewriting approaches is quite natural to use when modelling systems whose states have a network structure [1].…”