based on gap penalty function definition:
w(k)= h + gk, k>0
where h penalizes opening of a gap and is usually large ( -12 or so ), and g penalizes extension of a gap ( usually -2 or -3 )
1- Sketch a Dynamic Programming algorithm for the affine gap penalty case . Just stating the recurrence relations will suffice.
2- Comment of the types of effects on alignments produced if you varied h and g as follows:
h g effect? large large small large large small
Many Thanks,
Rico