Answer the following questions about substitution (scoring) matrices

a. why would a simplified scoring scheme (ie, +1 for any match, -1 for any mismatch, -2 for any gap) yield alignments of low quality/biological accuracy?

b. suppose we align two moderately diverged protein sequences with the simplified scoring matrix above, and unsatisfied with the results, we change the match score to +4 and mismatch score to -4. However, we do not adjust the gap penalty. What is the most likely effect of this revised scoring system of the alignment, relative to the original alignment?

A. resulting alignment will include more gaps

B. resulting alignment will contain more mismatches

C. resulting alignment will be shorter

D. resulting alignment won’t change much

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