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

Eran Elhaik, Dan Graur, Kresimir Josić

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)147
JournalComputational biology and chemistry
Volume32
Issue number2
DOIs
Publication statusPublished - 2008 Apr
Externally publishedYes

Free keywords

  • Base Composition
  • Base Sequence
  • Genome
  • Sequence Analysis, DNA

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