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The Structure of Elementary Strategies for Gene Assembly in Ciliates

Vladimir Rogojin, Ion Petre, The Structure of Elementary Strategies for Gene Assembly in Ciliates. Fundamenta Informaticae 137, 1–14, 2015.

http://dx.doi.org/10.3233/FI-2015-1199

Abstract:

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 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 operations applicable to a given permutation to paths in the dependency graph associated to that permutation.

BibTeX entry:

@ARTICLE{jRoPe15a,
  title = {The Structure of Elementary Strategies for Gene Assembly in Ciliates},
  author = {Rogojin, Vladimir and Petre, Ion},
  journal = {Fundamenta Informaticae},
  volume = {137},
  publisher = {IOS Press},
  pages = {1–14},
  year = {2015},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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