Alignment Parameters

In the last exercise, we saw that simple Dynamic Programming alignments are not always biologically relevant. One reason for this is that simple Dynamic Programming merely treats DNA and Protein sequences as strings of letters and cares nothing about insertions, deletions, or mutations.

The primary modifications that have been made to basic Dynamic Programming to help represent these biological processes are Gap Penalties and Scoring (or Substitution) Matrices, respectively. We will look at each of these parameters in this exercise.

Next - Gaps and Gap Penalties
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Up - Pairwise Sequence Alignments