Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

Details Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

2004-12-15

arxiv.org/abs/q-bio/0412028v2

Gene, Volume 347 (2) 175-182 (2005)

Biology

Quantitative Biology

Populations and Evolution

12 pages, 4 figures, corrected typos

Scientific paper

10.1016/j.gene.2004.12.019

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.

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