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Throughout the rest of this paper, we will use A T→G C to denote such a pair of nucleotide changes.
In the estimation of mutational spectrum, the frequencies in a pair of nucleotide changes (e.g., G→A and C→T) were close in most of the categories we investigated (Table 1).
Given a pair of nucleotide sequences with one taken to be derived from the other, an alignment between them is equivalent to an accounting of the mutations via which the derivation occurred.
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For each pair of base-pair unwound a pair of nucleotides (nt) is released.
When a pair of nucleotides in a repeat element have a positive substitution score, the product <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0011147.e054.PNG" class= inline-graphic"/> down-weights the score.
The substitution matrix score quantifies the log-odds ratio that a pair of nucleotides share common ancestry, but does not account for the inherent repetitive nature of genomic sequence.
Similar to other members of the ABC family, ABCF2 contains a pair of nucleotide-binding domains but it lacks a transmembrane domain (Allikmets et al, 1996; Kerr, 2004), suggesting that it is unlikely to function as a cell membrane transporter, as do other members of the ABC family.
Nonsynonymous divergence for a pair of nucleotides (A, B) was defined analogously to synonymous divergence.
The case (MP, MP) handles the emission of a pair of nucleotides.
Such genotype data contain for each individual and each assessed SNP a pair of nucleotides, reflecting the two alleles (maternal and paternal) of the individual.
When P i, j x, y was equal to 1.0, no preference for a pair of nucleotides x and y at positions i and j exists.
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