title: Controlled synthesis of target strings in a class of splicing systems.
abstract: This article presents an approach for synthesizing target strings in a class of computational models of DNA recombination. The computational models are formalized as splicing systems in the context of formal languages. Given a splicing system (of a restricted type) and a target string to be synthesized, we construct (i) a rule-embedded splicing automaton that recognizes languages containing strings embedded with symbols representing splicing rules, and (ii) an automaton that implicitly recognizes the target string. By manipulating these two automata, we extract all rule sequences that lead to the production of the target string (if that string belongs to the splicing language). An algorithm for synthesizing a certain type of target strings based on such rule sequences is presented.
authors.affiliation: Faculty of Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore. engchenp@nus.edu.sg
authors.forename: Peter C Y
authors.initials: PC
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D001331:Automation; D019295:Computational Biology; D003198:Computer Simulation; D003205:Computing Methodologies; D004247:DNA / Q000737:chemistry; D015233:Models, Statistical; D010363:Pattern Recognition, Automated; D012326:RNA Splicing; D011995:Recombination, Genetic; D012984:Software; D013597:Systems Analysis; D049490:Systems Biology; D013598:Systems Theory
chemical_list: D004247:DNA