Discussion:
In the global sequence alignment, what is the impact of the gap penalty?
When performing an alignment of two A A sequences. Dayhoff' s or another scoring matrix is used. Suppose, a gap penalty is delta. Given a scoring matrix. D[21][21]. the dynamic programming is to find a path(s) with the largest score, s. Write the core of the dynamic programming forming the for loops that update the score s with respect to the A score matrix D.
How is the process of finding the maximum cost path(s) in dynamic programming for the global alignment different from Dijkstra's shortest-path algorithm (pick node w with min cost P[w]; update costs of other nodes v by P[v] = min (P [v], P[w] + link_cos t(w. v)) (not including the difference between max and min) ?