In the Smith-Waterman algorithm, adding gap penalties to the top and left values encourages finding the best local alignment between sequences. It discourages introducing gaps at the beginning, focusing on high-scoring local alignments. This ensures accurate alignment by considering both sequence similarity and gap costs. Hope that clarifies things!
why did we add gap penalty to top and left value?
In the Smith-Waterman algorithm, adding gap penalties to the top and left values encourages finding the best local alignment between sequences. It discourages introducing gaps at the beginning, focusing on high-scoring local alignments. This ensures accurate alignment by considering both sequence similarity and gap costs. Hope that clarifies things!