Sequence Alignment - III. Chitta Baral. Scoring Model. When comparing sequences Looking for evidence that they have diverged from a common ancestor by a process of mutation and selection Basic mutational processes Substitutions; insertions; deletions (together referred to as gaps)
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qx1q x2 … X qy1qy2 …
= -ge + e + (log k - e) = - (e - log k) – (g – 1) e
= - d – (g-1) e where d = e – log k ## affine score