Your ASSIGMENT for this week is to apply these scoring concepts to the two short

Question

Your ASSIGMENT for this week is to apply these scoring concepts to the two short DNA sequences below. We will use a lowest-score-is-best approach, with a match score of 0, a mismatch score of 1, a gap cost of 5, and a gap-extension cost of 1. Calculate the scores for the three alignments shown below. Note that the periods in the second sequence of each alignment indicates a match to the first sequence at that position. This is a commonly used convention in alignments that allows you to quickly see where sequences differ. The dashes, of course, represent gaps.Tell me scores and identify which of the 3 alignments: top, middle, or bottom, is best for the scoring scheme proposed.

Explanation / Answer

the score is 5+5+1+1+1+1+1+1+1+1+1+1+1+1+1+1=24

the score is 5+1+1+5+1+1+1+1+1+1+1+1+1+1+1+1=24

the score is 1+1+1+5+1+1+1+1+1+1+1+1+1+1+1+1=20

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