Handbook of Formal Languages
Computation in Living Cells: Gene Assembly in Ciliates (Natural Computing Series)
Computation in Living Cells: Gene Assembly in Ciliates (Natural Computing Series)
Template-guided DNA recombination
Theoretical Computer Science - Descriptional complexity of formal systems
Useful Templates and Iterated Template-Guided DNA Recombination in Ciliates
Theory of Computing Systems
On computational properties of template-guided DNA recombination
DNA'05 Proceedings of the 11th international conference on DNA Computing
Iterated TGR languages: membership problem and effective closure properties
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
Formal Language Tools for Template-Guided DNA Recombination
Language and Automata Theory and Applications
Minimality in template-guided recombination
Information and Computation
| Hi-index | 0.00 |
Template-guided recombination (TGR) is a formal model for the DNA rearrangement which occurs in certain ciliates. In this paper, the equivalence problem for TGR is considered: given two sets of templates, is their action is the same for all operands? This question is motivated by molecular computation, as we view equivalence in TGR as a method for discerning whether modifications to the functioning of a ciliate via the set of templates has any effect on the rearrangement it defines. This motivation is also suggested by recent experiments into the role of RNA in the rearrangement of ciliate DNA. We give a language-theoretic characterization of equivalence which leads to decidability results for common language classes. In particular, we show a positive answer for regular sets of templates. For context-free sets of templates, the answer is negative. The same language-theoretic characterization also applies to intra-molecular TGR. The problem for iterated TGR remains open.