20 points
Assigned Thursday, February 26
Due Thursday, March 5 by 11:59pm
In this mini-homework, you are to construct a multiple alignment of the five sequences you created in the prior mini-homeworks, and then build a profile HMM of that alignment. The multiple alignment will be derived directly from the evolutionary tree of mini-homework 0.5, i.e., directly align all indels and substitutions as they occurred in your evolutionary process. Then, the profile HMM will be derived from this multiple alignment using the approach described in class, using Laplace's rule as a prior. Include a picture of your HMM, both the structure and parameters. You may employ a shorthand notation to represent common emission probabilities, e.g., if a match column only includes the amino acids "A" and "V", then you may use the shorthand notation "*" to represent the other 18 amino acids that will have the same emission probability.
Take your writeup and your model and add them to your sequence descriptions and alignments in your personal wiki, which is already linked in from the course wiki. Do not remove your previous results from your wiki; keep everything as a single, comprehensive document.