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.
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.
Zagordi
Osvaldo
O
Dipartimento di Scienze Fisiche Complesso Universitario di Monte Sant'Angelo via Cinthia, 80126 Napoli, Italy. zagordi@sissa.it
Lobry
Jean R
JR
D019943:Amino Acid Substitution / Q000235:genetics*; D000818:Animals; D004247:DNA / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D019143:Evolution, Molecular; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D014981:Xenopus / Q000235:genetics
D004247:DNA