A three-state model for DNA protein-coding regions.

IEEE Trans Biomed Eng 2006 Nov;53(11):2148-55

Signal Processing Laboratory, DETI/IEETA, University of Aveiro, 3810-193 Aveiro, Portugal.

It is known that the protein-coding regions of DNA are usually characterized by a three-base periodicity. In this paper, we exploit this property, studying a DNA model based on three deterministic states, where each state implements a finite-context model. The experimental results obtained confirm the appropriateness of the proposed approach, showing compression gains in relation to the single finite-context model counterpart. Additionally, and potentially more interesting than the compression gain on its own, is the observation that the entropy associated to each of the three base positions of a codon differs and that this variation is not the same among the organisms analyzed.

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http://ieeexplore.ieee.org/iel5/10/36082/01710155.pdf?arnumb
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http://dx.doi.org/10.1109/TBME.2006.879477DOI Listing
November 2006
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