Specific Information


  • The first HW assignment is now posted. It is due by 2pm on Tuesday 27/10/15.
  • The second HW assignment is now posted. It is due with the final.
  • Class Notes

    Supplementary Material

  • A model of evolutionary change in proteins. MO Dayhoff, RM Schwartz, BC Orcutt - Atlas of protein sequence and structure, 1978
  • Table 22 from Dayhoff et al.: marginal amino acid frequencies
  • Table from Figure 82 of Dayhoff et al.: scaled transition probability matrix for one step of the PAM chain
  • Sequences for global alignment exercise in Assignment #1
  • Forward, backward and Viterbi as well as sampling R functions for HMM
  • BLOSUM62 marginals
  • HMM output
  • Staff


    Grading Structure and Schedule (Uri's half)