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2008
ACM

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

8 years 10 months ago
'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 ...
Eran Elhaik, Dan Graur, Kresimir Josic
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where CANDC
Authors Eran Elhaik, Dan Graur, Kresimir Josic
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