We consider in this paper the assembly of micronuclear genes in stichotrichous ciliates to their ... more We consider in this paper the assembly of micronuclear genes in stichotrichous ciliates to their macronuclear form. We represent the micronuclear genes and all their intermediate forms from micro-to macro-as signed permutations, where integer i stands for the i -th MDS of the macronuclear gene and (i) over bar stands for the inverted form of that MDS; the macronuclear assembled gene is represented as the sorted permutation 1 2 ... n, while its micronuclear form is an arbitrary signed permutation. We focus on the elementary gene assembly model consisting of two operations on signed permutations: eh (elementary hairpin inverting) and ed (elementary double recombination); gene assembly is modeled in this framework as a permutation sorting process. The general problem we investigate is to give a characterization of all signed permutations that can be sorted by the elementary operations. We make progress towards a full solution for this problem by relating sequences of eh and ed operatio...
The simple intramolecular model for gene assembly in ciliates is partic- ularly interesting becau... more The simple intramolecular model for gene assembly in ciliates is partic- ularly interesting because it can predict the correct assembly of all avail- able experimental data, although it is not universal. The simple model also has a confluence property that is not shared by the general model. A previous formalization of the simple model through sorting of signed permutations is
We consider in this paper the assembly of micronuclear genes in stichotrichous ciliates to their ... more We consider in this paper the assembly of micronuclear genes in stichotrichous ciliates to their macronuclear form. We represent the micronuclear genes and all their intermediate forms from micro-to macro-as signed permutations, where integer i stands for the i -th MDS of the macronuclear gene and (i) over bar stands for the inverted form of that MDS; the macronuclear assembled gene is represented as the sorted permutation 1 2 ... n, while its micronuclear form is an arbitrary signed permutation. We focus on the elementary gene assembly model consisting of two operations on signed permutations: eh (elementary hairpin inverting) and ed (elementary double recombination); gene assembly is modeled in this framework as a permutation sorting process. The general problem we investigate is to give a characterization of all signed permutations that can be sorted by the elementary operations. We make progress towards a full solution for this problem by relating sequences of eh and ed operatio...
The simple intramolecular model for gene assembly in ciliates is partic- ularly interesting becau... more The simple intramolecular model for gene assembly in ciliates is partic- ularly interesting because it can predict the correct assembly of all avail- able experimental data, although it is not universal. The simple model also has a confluence property that is not shared by the general model. A previous formalization of the simple model through sorting of signed permutations is
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Papers by Ion Petre