'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve
Elhaik, Eran LU
; Graur, Dan
and Josić, Kresimir
(2010)
In Biology Direct
5.
- Abstract
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... (More)
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/ square root 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 the Z-curve.
RESULTS: In this work, we studied the basic properties of the Z-curve using the "genome order index" as a case study. We show that (1) the calculation of the radius of the inscribed sphere of a regular tetrahedron is incorrect, (2) the S index is narrowly distributed, (3) based on the second parity rule, the S index can be derived directly from the Shannon entropy and is, therefore, redundant, and (4) the Z-curve suffers from over dimensionality, and the dimension stands for GC content alone suffices to represent any given genome.
CONCLUSION: The "genome order index" S does not represent a constraint on nucleotide composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively.
(Less)
- author
- Elhaik, Eran
LU
; Graur, Dan
and Josić, Kresimir
- publishing date
- 2010-02-17
- type
- Contribution to journal
- publication status
- published
- keywords
- Base Composition/genetics, Base Sequence/genetics, Computer Simulation, Genome, Bacterial/genetics, Models, Genetic
- in
- Biology Direct
- volume
- 5
- article number
- 10
- pages
- 7 pages
- publisher
- BioMed Central (BMC)
- external identifiers
-
- scopus:77949456442
- pmid:20158921
- ISSN
- 1745-6150
- DOI
- 10.1186/1745-6150-5-10
- language
- English
- LU publication?
- no
- id
- 5409bf53-0354-47d6-b0ac-a8780ccf2413
- date added to LUP
- 2019-11-10 16:49:17
- date last changed
- 2024-01-01 23:32:46
@article{5409bf53-0354-47d6-b0ac-a8780ccf2413,
abstract = {{<p>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/ square root 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 the Z-curve.</p><p>RESULTS: In this work, we studied the basic properties of the Z-curve using the "genome order index" as a case study. We show that (1) the calculation of the radius of the inscribed sphere of a regular tetrahedron is incorrect, (2) the S index is narrowly distributed, (3) based on the second parity rule, the S index can be derived directly from the Shannon entropy and is, therefore, redundant, and (4) the Z-curve suffers from over dimensionality, and the dimension stands for GC content alone suffices to represent any given genome.</p><p>CONCLUSION: The "genome order index" S does not represent a constraint on nucleotide composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively.</p>}},
author = {{Elhaik, Eran and Graur, Dan and Josić, Kresimir}},
issn = {{1745-6150}},
keywords = {{Base Composition/genetics; Base Sequence/genetics; Computer Simulation; Genome, Bacterial/genetics; Models, Genetic}},
language = {{eng}},
month = {{02}},
publisher = {{BioMed Central (BMC)}},
series = {{Biology Direct}},
title = {{'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve}},
url = {{http://dx.doi.org/10.1186/1745-6150-5-10}},
doi = {{10.1186/1745-6150-5-10}},
volume = {{5}},
year = {{2010}},
}