Lecture 5 : Time speedup , General gap penalty function
نویسنده
چکیده
If we believe that the two sequences x and y are similar then we might be able to optimally align them faster. For simplicity assume that m = n since our sequences are similar. If x and y align perfectly, then the optimal alignment corresponds to the diagonal in the dynamic programming table (now of size n × n). This is because all of the back pointers will be pointing diagonally. Therefore, if x and y are similar, we expect the alignment not to deviate much from the diagonal. For instance, consider the following two sequences x = GCGCATGGATTGAGCGA and y = TGCGCCATGGATGAGCA. Their optimal alignment is shown below:
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