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
It might even make for better alignments.
johnk at jhunix.hcf.jhu.edu
I'm not an idiot, but I play one on USENET