I am now working on Smith-Waterman algorithm. I understand that by increasing the gap penalty, less gap will be obtained in my final alignment but I need advice on how to control the maximum gap rate (ratio of gapped character in the detected char)? For example:
Maximum gap rate: 50% Sequence 1: ABBBBC Sequence 2: ABC
Final alignment: AB---C
From the total length of the detected char, which is 6, it will detect up to 3 gapped char as similar alignments. Thank you.
