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Home > Problems > Chapter 5
7. Analyze the following ten DNA sequences by the Gibbs sampling algorithm.
seq1 C CAG A
seq2 G TTA A
seq3 G TAC C
seq4 T TAT T
seq5 C AGA T
seq6 T TTT G
seq7 A TAC T
seq8 C TAT G
seq9 A GCT C
seq10 G TAG A
- Assuming that the background base frequencies are 0.25, calculate a log odds matrix for the central three positions.
- Assuming that another sequence G TTT G is the left-out sequence, slide the log odds matrix along the left-out sequence and find the log odds score at each of three possible positions.
- Change each log odds score to an odds score and sum the odds scores. Calculate the probability of a match at each position in the left-out sequence. (Odds score = 2 raised to the power of the log odds score.)
- How do we choose a possible location for the motif in the left-out sequence?
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