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The loop regions of the RNA are specified in the alignment and may be modeled by either of the two single nucleotide foundation models (HKY + Г or GTR + Г).
Both nucleotide foundation models are always used in conjunction with Г-distributed rates-across-sites, indicated by a "+Г" suffix (Yang 1994).
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Nucleotides are the foundation of all physiological functions.
Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation.
Single nucleotide polymorphisms (SNPs) are the foundation of powerful complex trait and pharmacogenomic analyses.
These genetic maps, expanded with gene-specific single nucleotide polymorphisms (SNPs), provide a foundation for the investigation of the genomic regions underlying adaptive traits.
This study examines 18 different parameterizations of to define "foundation models" of nucleotide and dinucleotide evolution, which are later combined to provide a range of substitution models describing RNA evolution (discussed later).
It underlies mutational biases characteristic for genomes with different nucleotide and amino acid compositions, providing foundation for evolution and adaptation.
Identification of urinary nucleotide adducts using LC/MS has provided a foundation for large-scale monitoring studies of several genotoxic agents (Shuker and Farmer 1992; Singh and Farmer 2006) and could prove useful for brevetoxins as well.
To describe the evolution of independent nucleotides, we use two common (4-state) foundation models: 1) the HKY model (Hasegawa et al. 1985) and 2) the general time-reversible (GTR) model (Lanave et al. 1984; Tavaré 1986).
Second, Markov-process models of nucleotide substitution used in distance calculations lay a foundation for likelihood and Bayesian analyses.
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