'Genome order index' should not be used for defining compositional constraints in nucleotide sequences.
A "genome order index," defined as S=a(2)+c(2)+t(2)+g(2), where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively, was used to suggest that there exist genome-specific constraints on nucleotide composition. We show that the "evidence" for constraint, S<1/3, is in fact a mathematical property that is always true regardless of data. Moreover, we show that S is strictly equivalent to and derivable from the Shannon H-function and has no advantage over it.
Elhaik
Eran
E
Department of Biology & Biochemistry, University of Houston, Houston, TX 77204-5001, USA. eelhaik@gmail.com
Graur
Dan
D
Josić
Kresimir
K
D001482:Base Composition; D001483:Base Sequence; D016678:Genome; D017422:Sequence Analysis, DNA