problem 1: For an alignment shown below derive log-odds score for the column 1 only by:

a) Computing observed probability values.

b) Expected probability values.

TAGCTT
AAGCTC
T-GGTT
TGGCAT
TACCTT

problem 2: Using 1st order models determine the probability of coding region in frame two for DNA fragment AGTAGCTTCCAG. Use only parameters provided in the homework solution. Show all of your work.

problem 3: For the zero order hidden Markov model determine probability of coding state at the last nucleotide of the sequence AGTAG. Use parameters provided in the homework solution. Show all of your work.

problem 4: p-value and e-value are used to assess the significance of the alignment. Can you think of additional ways of evaluating the strength of the alignment other than bit Score?