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In biology, a substitution model, also called models of sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules, such as DNA sequences or protein sequences, that can be represented as sequence of symbols (e.g., A, C, G, and T in the case of DNA or the 20 "standard" proteinogenic amino acids in the case of ...
The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a G/A polymorphism) In genetics and bioinformatics, a single-nucleotide polymorphism (SNP / s n ɪ p /; plural SNPs / s n ɪ p s /) is a germline substitution of a single nucleotide at a specific position in the genome.
Point substitution mutations of a codon, classified by their impact on protein sequence. A synonymous substitution (often called a silent substitution though they are not always silent) is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified.
One PAM unit is defined as 1% of the amino acid positions that have been changed. To create a PAM1 substitution matrix, a group of very closely related sequences with mutation frequencies corresponding to one PAM unit is chosen. Based on collected mutational data from this group of sequences, a substitution matrix can be derived.
A conservative replacement (also called a conservative mutation or a conservative substitution or a homologous replacement) is an amino acid replacement in a protein that changes a given amino acid to a different amino acid with similar biochemical properties (e.g. charge, hydrophobicity and size).
Missense mutation is a type of nonsynonymous substitution in a DNA sequence. Two other types of nonsynonymous substitution are the nonsense mutations , in which a codon is changed to a premature stop codon that results in truncation of the resulting protein , and the nonstop mutations , in which a stop codon erasement results in a longer ...
A substitution of one amino acid for another can impair protein function and tertiary structure, however its effects may be minimal or tolerated depending on how closely the properties of the amino acids involved in the swap correlate. [11] The premature insertion of a stop codon, a nonsense mutation, can alter the primary structure of a ...
Genetic saturation is the result of multiple substitutions at the same site in a sequence, or identical substitutions in different sequences, such that the apparent sequence divergence rate is lower than the actual divergence that has occurred. [1]