homology, similarity and identity....

moreaut at univ-tours.fr moreaut at univ-tours.fr
Thu Feb 3 10:53:19 EST 1994

dear colleagues,

I would like to have your point of view on the problem of sequence 
homology, sequence similarity and percent identity.

When I align two related proteins with Gap or Bestfit in the GCG package,
the % identity and % similarity vary between about 35 to 50 % identity.
This percentage obviously depends of the gap parameters chosen for this 
alignment. OK

I would like to know what is the best thing to do to quantify the alignment
is it better to give a range for the % identity or is it better to give
% identity for different sections of the 2 proteins ?
Same questions for homology and/or similarity ?

I should be happy to get clear definitions on homology, similarity
and identity percentages

Thanks in advance for any suggestions

Thierry MOREAU
Laboratoire d'Enzymologie et Chimie des Proteines 
TOURS  France

Email: moreaut at univ-tours.fr


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