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For example, I have two sequences (one is longer or equal to another) and I want to make a global alignment between them, but I only want to generate gaps in the shorter sequence. I see that the GapsMis can somehow do it in O(m*k) where m = shorter sequence length and k = number of gaps. But I have a hard time understanding it. Can anyone explain it more clearly or could have a better methods? Very appreciated!

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