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Sulfadoxine-pyrimethamine was the first line anti-malarial drug used until early 2006 when the artemisinin base combination therapy (artemether-lumefantrine) was introduced throughout Kenya.
All 17 base tags began with the four base combination 'GATC' to ensure that all matches occurred immediately downstream of a DpnII site.
A limiting aspect of this approach however is that the neighbouring base combination is assumed not to change along the length of a branch.
For the model parameters of each context (i.e. neighbouring base combination) independently, the following prior distribution is assumed (see e.g. [ 27]): Further, branch lengths are assumed i.i.d.i.d
The specific base combination CAG (repeated at least 7 times) is found in 1815 genes, leading to conceptual translations into homopolymeric amino acid repeats (HAARs) of alanine (A), glutamine (Q) or serine (S) in 1781 (30%) proteins.
Contrary to the original context-dependent model developed for non-coding sequences [ 13], the evolution of the third codon position could be allowed to depend upon the neighbouring base combination at both the start and the end of each branch.
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In principle, there are 4 n base combinations for the input and output molecules, where n denotes the length of the signalling molecule.
Additionally, MRI was generally observed with other base combinations and single bases.
We then add probabilities for the same scores resulting from different base combinations.
It shows large variation in substitution rates across different neighbouring base combinations.
For l = 5, each gene had 1,024 (= 4) different base combinations.
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