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

Armando J Pinho; António J R Neves; Vera Afreixo; Carlos A C Bastos; Paulo J S G Ferreira

doi:10.1109/tbme.2006.879477

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

Armando J Pinho·António J R Neves·Vera Afreixo·Carlos A C Bastos·Paulo J S G Ferreira

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Abstract

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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Algorithms Base Sequence Computer Simulation DNA Models, Genetic Molecular Sequence Data Open Reading Frames Proteins Sequence Alignment Sequence Analysis, DNA Journal Article Research Support, Non-U.S. Gov't

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Armando J Pinho, António J R Neves, Vera Afreixo, Carlos A C Bastos, Paulo J S G Ferreira. 2006. A three-state model for DNA protein-coding regions.. https://doi.org/10.1109/tbme.2006.879477

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