correct use of homology-identity-similarity ?

theodorn at theodorn at
Mon Nov 30 12:00:38 EST 1998

In article <Pine.A41.4.05.9811292315390.42260-100000 at>,
  "Carsten Hohoff" <hohoff at> wrote:
> Where can I find the definition of 'homology', 'similarity' and 'identity'
> in sequence alignments ?
> We just had a discussion in the lab about this topic - I thought, 'identical'
> amino acid means the same aa, while  'similar' means a related (e.g., basic,
> acid, hydrophobic etc.) and 'homolog' is just a rough description of a
> relationship based on sequence alignment...
> Any hints that could help clarifying these terms are highly appreciated
> Best regards
> Carsten Hohoff

I was taught that "homologous" was a term that meant that two features
(sequences, whatever) were related by evolutionary descent.  Things were
either "homologous" with each other or not.  For degrees of similarity, one
should say "percent amino acid identity" or "percent amino acid similarity"
or something along those lines, but not "percent homology."  IIRC, my
"advisor-in-law" (i.e., my wife's Ph.D thesis advisor), Emmanuel Margoliash,
who had an interest in molecular phylogeny, was pretty adamant about the
misuse of the term "homology."

Nick Theodorakis

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