Difference between homology, identity and similarity

[Dr. Ram Samudrala]

"Anonymous at Organon.oss.akzonobel.nl" <anonymous at organon.oss.akzonobel.nl> wrote:

>Could someone explain to me the difference between protein sequence
>homology, identity, and similarity ?

It depends on the context.  Some people would say that homology means
that the sequences are evolutionarily related, identity is the
fraction of amino acids that are the same between a pair of sequences
after an alignment of the sequences (which can be done using only
sequence information or structural information or some other
information, but usually it is based on sequence information alone),
and similarity is the score assigned based on an alignment using some
similarity matrix.

Some people use homology and identity interchangeably (most notably,
Branden and Tooze, p249 (caption) in Introduction to Protein
Structure).  Others may say homology is more akin to similarity and
use those interchangeably (this is something I particularly noticed at
CASP, see Proteins: Structure Function Genetics Supplemental 1, 1997).

I am not one of those people who thinks that the usage has to be one
way or another (particularly with regards to what "homology" is). As I
say above, I think it depends on the context and as long as it is
clear (from the context or from an explicit statement) what people
mean, that's all that's necessary.

--Ram

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