Ion Petre
University of Turku, Department of Mathematics, Faculty Member
- Åbo Akademi, Department of Computer Science, Faculty Memberadd
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ABSTRACT
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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... 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...
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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... 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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The way that ciliates transform genes from their micronuclear to the macronuclear form is very interesting (and unique), also from a computational point of view. In this paper, we describe the model of gene assembly in ciliates presented... more
The way that ciliates transform genes from their micronuclear to the macronuclear form is very interesting (and unique), also from a computational point of view. In this paper, we describe the model of gene assembly in ciliates presented in (2), (3), and (4). Moreover, we prove that the set of three operations underlying this model is universal, in the sense
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Over the past years there has been quite a lot of activity in the algebraic community about using algebraic methods for providing support to model-driven software engineering. The aim of this workshop is to gather researchers working on... more
Over the past years there has been quite a lot of activity in the algebraic community about using algebraic methods for providing support to model-driven software engineering. The aim of this workshop is to gather researchers working on the development and application of algebraic methods to provide rigorous support to model-based software engineering. The topics relevant to the workshop are all those related to the use of algebraic methods in software engineering, including but not limited to: formally specifying and verifying model-based software engineering concepts and related ones (MDE, UML, OCL, MOF, DSLs, ...); tool support for the above; integration of formal and informal methods; and theoretical frameworks (algebraic, rewriting-based, category theory-based, ...). The workshop's main goal is to examine, discuss, and relate the existing projects within the algebraic community that address common open-issues in model-driven software engineering.