A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
Simple gene assembly as a rewriting of directed overlap-inclusion graphs
Tekijät: Azimi S, Harju T, Langille M, Petre I
Kustantaja: ELSEVIER SCIENCE BV
Julkaisuvuosi: 2012
Journal: Theoretical Computer Science
Tietokannassa oleva lehden nimi: THEORETICAL COMPUTER SCIENCE
Lehden akronyymi: THEOR COMPUT SCI
Vuosikerta: 454
Aloitussivu: 30
Lopetussivu: 37
Sivujen määrä: 8
ISSN: 0304-3975
DOI: https://doi.org/10.1016/j.tcs.2012.04.018
Rinnakkaistallenteen osoite: https://research.utu.fi/converis/portal/detail/Publication/2526512
Tiivistelmä
The simple intramolecular model for gene assembly in ciliates consists of three molecular operations, simple Id, simple hi and simple dlad. Mathematical models in terms of signed permutations and signed strings proved limited in capturing some of the combinatorial details of the simple gene assembly process. Brijder and Hoogeboom introduced a new model in terms of overlap-inclusion graphs which could describe two of the three operations of the model and their combinatorial properties. To capture the third operation, we extended their framework to directed overlap-inclusion (DOI) graphs in Azimi et al. (2011) [1]. In this paper we introduce DOI graph-based rewriting rules that capture all three operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. (C) 2012 Elsevier B.V. All rights reserved.
The simple intramolecular model for gene assembly in ciliates consists of three molecular operations, simple Id, simple hi and simple dlad. Mathematical models in terms of signed permutations and signed strings proved limited in capturing some of the combinatorial details of the simple gene assembly process. Brijder and Hoogeboom introduced a new model in terms of overlap-inclusion graphs which could describe two of the three operations of the model and their combinatorial properties. To capture the third operation, we extended their framework to directed overlap-inclusion (DOI) graphs in Azimi et al. (2011) [1]. In this paper we introduce DOI graph-based rewriting rules that capture all three operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. (C) 2012 Elsevier B.V. All rights reserved.
Ladattava julkaisu This is an electronic reprint of the original article. |  |
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