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1. Log odds and odds score of a short alignment. This question is a continuation of the question in Part III in Chapter 3 (p. 119).
  1. Using the values calculated in Part III, Chapter 3, what is the log odds score of the following alignment in bits? (Note that these two short sequences have very low sequence complexity by having only two amino acids of the available 20. These sequences were chosen to simplify the calculations. Such alignments are quite high scoring, but the low complexity means that the score can be misleading as discussed in Chapter 5, p. 254.)
  2. What is the odds score of the following alignment?
  3. Using the section "Quick Determination of the Significance of an Alignment Score" (p. 139), and assuming that the above alignment was found by aligning two sequences of length 250, is the alignment significant at the 0.05 level? (That is, could an alignment of two random sequences of the same length achieve such a score with a probability of 0.05?)
  4. If the gap penalty was very high, e.g., gap opening of 8 and gap extension of 8, so that no gaps were produced, and the BLOSUM62 scoring matrix was used, calculate the significance of the alignment using Equation 8. You will need to find the value of K and λ in Table 4.3 (p. 142) and note that λ in this table assumes that the alignment score is in half-bits so that the alignment score must be in these units also.


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