Dear Modellers,
I am working on a structural alignment between 6 protein structures with
an average seq. identity of approx. 25 % and average homology of approx.
45 %. Usage of default values for gap creation and extension penalties
for structure/structure superposition (0.0 and 1.75 respecrtively)
result in the introduction of multiple (relatively) large gaps in the
multiple sequence alignment. Of course I can "avoid" this by increasing
both gap creation and extension penalties, but what I would like to know
which penalty values are "reasonable" in this case.
Thanking you in advance and with kind regards,
Chris de Graaf
--
drs. C. de Graaf
LACDR - Division Molecular Toxicology
Department Pharmacochemistry
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
Tel. (31) 020-4447608
Fax. (31) 020-4447610