Rewriting rule chains modeling DNA rearrangement pathways

We introduce a model that describes rearrangement pathways of DNA recombination events. The recombination processes may happen in a succession, possibly with some recombination events performed simultaneously, but others in a prescribed order. These events are modeled by three rewriting rules applie...

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Bibliographic Details
Published in:Theoretical computer science 2012-10, Vol.454, p.5-22
Main Authors: Angeleska, Angela, Jonoska, Nataša, Saito, Masahico
Format: Article
Language:English
Subjects:
Assembly pathways
Ciliates
DNA rearrangement
Rewriting rules
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Summary:We introduce a model that describes rearrangement pathways of DNA recombination events. The recombination processes may happen in a succession, possibly with some recombination events performed simultaneously, but others in a prescribed order. These events are modeled by three rewriting rules applied on a set of formal linear and circular words. We define a partial order on these sets in such a way that two sets are related by this order when molecules represented by one are produced by recombination events from the other. We apply our model to experimental data obtained for DNA rearrangement of the actin I gene in O. trifallax ciliates, and we predict possible pathways of gene rearrangement compatible with the data.
ISSN:0304-3975
1879-2294
DOI:10.1016/j.tcs.2012.04.041