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

From OpenWetWare

Jump to: navigation, search

Contents

Nicolas Rodrigue : Bayesian comparisons of codon substitution models

Tue Jun 26 12:39:33 EDT 2007

Words to Look Up

Talk

Questions

Corolin Kosoil : Empirical codon models and natural selection

Tue Jun 26 13:02:32 EDT 2007

  • Bustamante group - Cornell
  • Ian Holmes - Berkeley

Words to Look Up

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?
Personal tools