TY - JOUR
T1 - 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences
AU - Elhaik, Eran
AU - Graur, Dan
AU - Josić, Krešimir
N1 - Funding Information:
KJ was supported in part by NSF Grant DMS-0071735. DG and EE were supported in part by NSF Grant DBI-0543342. We wish to thank the Editors of CBAC for carefully reading the manuscript and suggesting its current format.
PY - 2008/4
Y1 - 2008/4
N2 - A "genome order index," defined as S = a2 + c2 + t2 + g2, 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.
AB - A "genome order index," defined as S = a2 + c2 + t2 + g2, 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.
KW - Genome order index
KW - Genomic G + C content
KW - Isochores
KW - Nucleotide composition
KW - Shannon H-function
UR - https://www.scopus.com/pages/publications/40049085288
U2 - 10.1016/j.compbiolchem.2007.11.003
DO - 10.1016/j.compbiolchem.2007.11.003
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AN - SCOPUS:40049085288
SN - 1476-9271
VL - 32
SP - 147
JO - Computational Biology and Chemistry
JF - Computational Biology and Chemistry
IS - 2
ER -