I am trying to determine that how my sequence(probe) "hits" against a long sequence(genome). The LongestCommonSubsequence in Mathematica gives the first longest common subsequence between two sequences. Is there a good way to find the second longest common subsequence between two sequences? ( Once the probe hits somewhere with longest common subsequence, it will not hit the same region anymore, so that the longest commonsubsequence -1 shouldn't be considered)
I am thinking that one possible way is drop or delete the first longest common subsequence from the long sequence (genome) and run LongestCommonSubsequence again. But obviously this will be really slow considering the genome sequence is big.