Smith Waterman Algorithm For local Alignment || Dynamic programming || Bioinformatics

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[@5a3i67]

Great explanation

[@BioScholar971]

thanks

[@waynemazonde654]

is the affine gap penalty for local alignment

[@BioScholar971]

Affine gap penalties are well-suited for local alignment because they discourage the algorithm from opening too many small gaps, which are less likely to be significant in local alignment. Global alignment algorithms, on the other hand, are more likely to tolerate small gaps. However, affine gap penalties can still be used for global alignment, and they are often used in conjunction with a global alignment algorithm to find the best alignment between two sequences, even if the sequences contain long gaps.

[@yusuft.3587]

I didnt understant how we calculate dioagonal value

[@BioScholar971]

"When two letters match, we increment the diagonal value by a match reward. However, in case of a mismatch, we add a specified mismatch penalty to the diagonal value." If you have any other question feel free to ask.

[@waynemazonde654]

diagonal value u add a match value to value in the diagonal box or a mismatch value if its a mismatch. for side and below value and a gap penalty value.