Advanced Bioinformatics Workshop - Winter 2001 - Final

• Sequence Alignment of AGAWGHEE and APGYAHE: What is the Needleman/Wunsch Dynamic Programming Matrix and the resulting alignment when...
  • ... using an identity scoring matrix (original NW)
  • ... using the BLOSUM50 matrix and -8 as gap penalty (NW - Gotoh)
• What are the main differences between the PAM and BLOSUM matrices (name at least two individual characteristics)
• Using the Biology Workbench's ClustalW interface, generate the multiple sequence alignment for the following sequences (attach resulting page):
  • ACAATG
  • TCAACTATC
  • AGACTGC
  • AGAATC
  • ACCGATC
• What is the log-odds score for TGCTAGG using the alignments on slide 18 and 19 of the HMM lecture?
• What is the total likelihood of rolling a 4 twice in a row, for all possible state sequences? (use the HMM given on slide 23)