The problem of RNA secondary structure design is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. Here, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on well-known concepts of language theory, namely context-free grammars and finite state automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size.
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