Julius B. Lucks/Meetings and Notes/SMBE2007/models protein evolution 1

= Nicolas Rodrigue : Bayesian comparisons of codon substitution models = Tue Jun 26 12:39:33 EDT 2007

Questions
= Corolin Kosoil : Empirical codon models and natural selection = Tue Jun 26 13:02:32 EDT 2007
 * Bustamante group - Cornell
 * Ian Holmes - Berkeley

Talk

 * used to select positive selecction
 * omega - defined as the nonsynonymous/synonymous rate ratio
 * < 1 - purifying selection
 * == 1 - neutral evolution
 * > 1 - positive selection

Questions
= Richard Goldstein : Mon-equilibrium models - modeling the evolution of extremophiles = Tue Jun 26 13:34:37 EDT 2007

Words to Look Up

 * Levy skew alpha stable distribution
 * Gassian special case
 * lorentzian special case
 * big tails
 * more gen central limit theorum

Talk

 * can treat evolution of Optimal Growth Temperature within a phylogenetic framework
 * chonges in OGT in Bact and archaea show strongly non-normal behav
 * large skew - non-neg tail
 * GC content (avg over codens) does not chang much w/ AA comp change
 * interesting changes in composition, reflecting T-dependence of intramolecular interactions
 * mentioned Shakhnovich PLoS Comp Bio paper

Questions

 * compare thermophiles to antifreeze proteins?