Exploring Homology Using the Concept of Three-State Entropy Vector Authors: Armando J. Pinho, Sara P. Garcia, Paulo J. S. G. Ferreira, Vera Afreixo, Carlos A. C. Bastos, António J. R. Neves, João M. O. S. Rodrigues Keywords: DNA signature, DNA coding regions, DNA entropy, Markov models
Abstract:
The three-base periodicity usually found in exons has been used for several purposes, as for example the prediction of potential genes. In this paper, we use a data model, previously proposed for encoding protein-coding regions of DNA sequences, to build signatures capable of supporting the construction of meaningful dendograms. The model relies on the three-base periodicity and provides an estimate of the entropy associated with each of the three bases of the codons. We observe that the three entropy values vary among themselves and also from species to species. Moreover, we provide evidence that this makes it possible to associate a three-state entropy vector with each species, and we show that similar species are characterized by similar three-state entropy vectors.
I include this paper both as informative for the bioinformatics crowd as well as to illustrate that subject identity tests are as varied as the subjects they identify. In this particular case, the identification of species for the construction of dendograms.