Homology and analogy
It is important to understand a concept that underpins sequence analysis - homology. The term homology is confounded and abused in the literature. Simply, sequences are said to be homologous if they are related by divergence from a common ancestor. Understanding homology allows us to appreciate the concept of analogy; this is encountered in protein structures that share similar folds but have no demonstrable sequence similarity; or that share groups of catalytic residues with almost exactly equivalent spatial geometries, but otherwise have neither sequence nor structural similarity. Such relationships are thought to result from convergence to similar biological solutions from different evolutionary starting-points. The essence of sequence analysis is the inference of homology. Homology is not a measure of similarity, but an absolute statement that sequences have a divergent rather than a convergent relationship. Thus, phrases that quantify homology are meaningless.

Orthology and paralogy
Homologous proteins may perform the same function in different species (orthologues) or different but related functions within one organism (paralogues). Comparison of orthologues allows study of molecular palaeontology, while paralogues have provided deeper insights into the underlying mechanisms of evolution. Paralogues arose from single genes via successive duplication events. The duplicated genes followed separate evolutionary pathways, and new specificities evolved through variation and adaptation.

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