correct use of homology-identity-similarity ?

Vladimir Svetlov svetlov at oncology.wisc.edu
Mon Nov 30 15:59:36 EST 1998


In article
<Pine.A41.4.05.9811292315390.42260-100000 at asterix.uni-muenster.de>,
"Carsten Hohoff" <hohoff at uni-muenster.de> 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

Firstly, if the terms originated with particular computer-assisted
alignment/philogeny program, consult the manual/original paper/designers
for definitions - you'd be surprised what a range of meanings the term
"similar" can take. Often similar means "within so many units from..."
according to a particular similarity scoring table (like BLOSUM or PAM). In
the literature there is a great discordance as to what amino acids are
"similar" and this is reflected in the assessment of similarity by various
programs out there.
Secondly, according to conventional wisdom in a given field the word
"homolog" can mean different things - from simple statement of sequence
similarity to a documented evolutionary relationship with all that
homotopy, homonomy and stuff.
So it depends on how rigorous you wanna be in using this term.

Cheers,
V.

-- 
Vladimir Svetlov, PhD
McArdle Lab for Cancer Res.
UW-Madison
1400 University Ave.
Madison, WI 53706



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