'Genome order index' should not be used for defining compositional constraints in nucleotide sequences
Elhaik, Eran LU
; Graur, Dan
and Josić, Kresimir
(2008)
In Computational biology and chemistry
32(2).
p.147-147
- Abstract
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.
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/fa418796-dd67-4dc9-ba66-43984fcd0796
- author
- Elhaik, Eran
LU
; Graur, Dan
and Josić, Kresimir
- publishing date
- 2008-04
- type
- Contribution to journal
- publication status
- published
- keywords
- Base Composition, Base Sequence, Genome, Sequence Analysis, DNA
- in
- Computational biology and chemistry
- volume
- 32
- issue
- 2
- pages
- 147 - 147
- publisher
- Elsevier
- external identifiers
-
- pmid:18243804
- scopus:40049085288
- ISSN
- 1476-9271
- DOI
- 10.1016/j.compbiolchem.2007.11.003
- language
- English
- LU publication?
- no
- id
- fa418796-dd67-4dc9-ba66-43984fcd0796
- date added to LUP
- 2019-11-10 16:54:25
- date last changed
- 2024-01-01 23:34:18
@article{fa418796-dd67-4dc9-ba66-43984fcd0796,
abstract = {{<p>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.</p>}},
author = {{Elhaik, Eran and Graur, Dan and Josić, Kresimir}},
issn = {{1476-9271}},
keywords = {{Base Composition; Base Sequence; Genome; Sequence Analysis, DNA}},
language = {{eng}},
number = {{2}},
pages = {{147--147}},
publisher = {{Elsevier}},
series = {{Computational biology and chemistry}},
title = {{'Genome order index' should not be used for defining compositional constraints in nucleotide sequences}},
url = {{http://dx.doi.org/10.1016/j.compbiolchem.2007.11.003}},
doi = {{10.1016/j.compbiolchem.2007.11.003}},
volume = {{32}},
year = {{2008}},
}