'Genome order index' should not be used for defining compositional constraints in nucleotide sequences

Background: The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as S = a2 + c2 +t2 +g2 , where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than 1/3 for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius r = 1/ 3 contains almost all points corresponding to various genomes, implying that S < r2 . The distribution of the points P obtained by S was studied using ...

• Type: Journal
• Year: 2008
• Where: CANDC
• Authors: Eran Elhaik, Dan Graur, Kresimir Josic
• Keywords: CANDC 2008, Emerging Technology, Genome, Genome Order Index, Z-curve