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over a longer period of evolutionary time. Each amino acid is more or less likely to mutate into various other amino acids. For instance, a [[hydrophilic]] residue such as [[arginine]] is more likely to be replaced by another hydrophilic residue such as [[glutamine]], than it is to be mutated into a [[hydrophobic]] residue such as [[leucine]]. (Here, a residue refers to an amino acid stripped of a hydrogen and/or a [[hydroxyl group]] and inserted in the [[polymer|polymeric chain]] of a protein.) This is primarily due to redundancy in the [[genetic code]], which translates similar codons into similar amino acids. Furthermore, mutating an amino acid to a residue with significantly different properties could affect the [[protein folding|folding]] and/or activity of the protein. This type of disruptive substitution is likely to be
If we have two amino acid sequences in front of us, we should be able to say something about how likely they are to be derived from a common ancestor, or [[Sequence homology|homologous]]. If we can line up the two sequences using a [[sequence alignment]] algorithm such that the mutations required to transform a hypothetical ancestor sequence into both of the current sequences would be evolutionarily plausible, then we'd like to assign a high score to the comparison of the sequences.
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