4B. DNA 2: Dynamic Programming, Blast, Multi-alignment, Hidden Markov Models

Welcome back to the second half, where we’ll talk about multisequence alignment, for starters. This leads to the issue of finding genes, a particular type of distant sequence comparison. The ones interested in is finding motifs that are involved in finding genes. And finally, we’ll end on hidden Markov model, the simplest one that I could think of that would really illustrate the idea of Markov models, probabilistic models, and the hiddenness.