A three-state model for DNA protein-coding regions.
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.
Pinho
Armando J
AJ
Signal Processing Laboratory, DETI/IEETA, University of Aveiro, 3810-193 Aveiro, Portugal. ap@det.ua.pt
Neves
António J R
AJ
Afreixo
Vera
V
Bastos
Carlos A C
CA
Ferreira
Paulo J S G
PJ
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D011506:Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D011506:Proteins; D004247:DNA