Protein Melting temerpature and ancient life.

Yesterday I was introduced to protein melting temperature.  Many things can cause a protein to denature(unfold).  Temperature is one of those causes.  Life needs to have proteins within a certain range below their melting point.  I don't know the details right now.  The part I found most interesting is how scientists have built clades from DNA sequences then predicted the most likely ancestor sequences then used them to build proteins.  From http://news.ufl.edu/2003/09/17/ancientprotein/, a 2003 paper concerning one such reconstruction, one can infer the temperature of the ancestor's habitat.  Since that 2003 the field has progressed.  It appears this technique maps closely to other techniques for determining world temperature in the distant past.

When introduced to Hamming distance, the number of changes needed to convert one sequence into another, I wrote this simple implementation:

def HamDist(s,t): return sum([1 for i in range(len (s)) if s[i] != t[i]])

It works and is easily understood.  I found this from http://code.activestate.com/recipes/499304-hamming-distance/.   I'm not sure I like summing truth values.

from itertools import imap 
import operator 
def HamDist(str1, str2): return sum(imap(operator.ne, str1, str2))

I'm learning pretty quickly.  There's a lot to learn.  I guess once one learns the language the faster code is readable.

Knowing the Hamming distance between a set of DNA, RNA, or AA sequences is the first step to building an un-rooted tree and this is the first step towards reconstructing the most likely ancestor sequences.