An important concept in sequence analysis is sequence homology. When two
sequences are descended from a common evolutionary origin, they are said to have a homologous relationship or share homology.
A related but different term is sequence similarity, which is the percentage of aligned residues that are similar in physiochemical properties such as size, charge, and hydrophobicity.
Generally, if the sequence similarity level is high enough, a common evolutionary relationship can be inferred. In dealing with real research problems, the issue of at what similarity level can one infer homologous relationships is not always clear. The answer depends on the type of sequences being examined and sequence lengths.
Shorter sequences require higher cut-offs for inferring homologous relationships than longer sequences. For determining a homology relationship of two protein sequences, for example, if both sequences are aligned at full length, which is 100 residues long, an identity of 30% or higher can be safely regarded as having close homology. They are sometimes referred to as being in the “safe zone”. If their identity level falls between 20% and 30%, determination of homologous relationships in this range becomes less certain. This is the area often regarded as the “twilight zone,” where remote homologs mix with randomly related sequences.
Below 20% identity, where high proportions of non-related sequences are present, homologous relationships cannot be reliably determined and thus fall into the “mid-night zone.”
sequences are descended from a common evolutionary origin, they are said to have a homologous relationship or share homology.
A related but different term is sequence similarity, which is the percentage of aligned residues that are similar in physiochemical properties such as size, charge, and hydrophobicity.
Generally, if the sequence similarity level is high enough, a common evolutionary relationship can be inferred. In dealing with real research problems, the issue of at what similarity level can one infer homologous relationships is not always clear. The answer depends on the type of sequences being examined and sequence lengths.
Shorter sequences require higher cut-offs for inferring homologous relationships than longer sequences. For determining a homology relationship of two protein sequences, for example, if both sequences are aligned at full length, which is 100 residues long, an identity of 30% or higher can be safely regarded as having close homology. They are sometimes referred to as being in the “safe zone”. If their identity level falls between 20% and 30%, determination of homologous relationships in this range becomes less certain. This is the area often regarded as the “twilight zone,” where remote homologs mix with randomly related sequences.
Below 20% identity, where high proportions of non-related sequences are present, homologous relationships cannot be reliably determined and thus fall into the “mid-night zone.”
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