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
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Thierry MOREAU
URA CNRS 1334
Laboratoire d'Enzymologie et Chimie des Proteines
TOURS France
Email: moreaut at univ-tours.fr
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