I remember a few posts (before the current thread began) about how to
calculate the "cost" of an insertion during sequence comparisons. In
general, the cost is of the form a + bx, where a is a constant cost
for making any insertion, b is the cost per inserted residue, and x is
the number of residues inserted.
This doesn't seem to make a whole lot of sense. An insertion at a site
on the surface of a protein should be a lot less expensive to make than
at an interior site.
Are there programs that, given a particular structure, will find sequence
relatives (ala David Eisenberg), using a cost function that varies with the
three-dimensional position of the insertion? Since residue exposure is
one of Eisenberg's environment criteria, this should be straightforward to
implement.
It might even make for better alignments.
--
John Kuszewski
johnk at jhunix.hcf.jhu.edu
I'm not an idiot, but I play one on USENET
