Your opinion as to what homolgy is

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Main Question or Discussion Point

In your opinion, do you think the word "homologous" is quantitative or qualitative?

That is, if I said "Sequence A is 95% homologous to sequence B!" would that be a correct or incorrect usage of the term?
 

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Ygggdrasil
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I think that the word homology is more of a qualitative term. Basically, if two sequences are homologous, they derived from a common ancestral sequence. You could split homology into two categories: paralogy and orthology. Orthologous genes are genes that play the same role in different organisms whereas paralogous genes are genes that derive from the a common ancestor but have diverged in function.

A statement like "sequence A is 95% homologous to sequence B" is commonly used and it could be considered correct. It can be somewhat ambiguous because there is a distinction between sequence identity (i.e. regions where sequence A and sequence B code for exactly the same amino acids) and sequence similarity (i.e. regions where sequence A and sequence B code for amino acids with the same chemical properties). Sequence homology is usually interpreted to mean the latter, though it would be better to specify whether one is looking at sequence similarity or sequence identity.
 
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A statement like "sequence A is 95% homologous to sequence B" is commonly used and it could be considered correct. It can be somewhat ambiguous because there is a distinction between sequence identity (i.e. regions where sequence A and sequence B code for exactly the same amino acids) and sequence similarity (i.e. regions where sequence A and sequence B code for amino acids with the same chemical properties). Sequence homology is usually interpreted to mean the latter, though it would be better to specify whether one is looking at sequence similarity or sequence identity.
I think it is better to use phrases such as "The sequences are x% identical indicating that they are homologous", alternatively "x% similar under y scoring scheme". In undergraduate courses at my university the professors are very keen to stress that it is not sensible to talk about degrees of homology, and urge us to use this term as a strictly binary label: two entities are either homologous or not. They (the professors) also tend to apologize that some of the available literature is written without proper regard to this.

Because of gene shuffling it might make sense to talk about partial homology in the sense that z% of a sequence is shown to be significantly similar to some other sequence, suggesting that a subsequence of a sequence is homologous to some part of another sequence, while the rest of the sequence is not (or at least is more distantly related).
 

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