A maximal common subsequence (MCS) between two strings X and Y is an inclusion-maximal subsequence of both X and Y. MCSs are a natural generalization of the classical concept of longest common subsequence (LCS), which can be seen as a longest MCS. We study the problem of efficiently listing all the distinct MCSs between two strings. As discussed in the paper, this problem is algorithmically challenging as the same MCS cannot be listed multiple times: for example, dynamic programming [Fraser et al., CPM 1998] incurs in an exponential waste of time, and a recent algorithm for finding an MCS [Sakai, CPM 2018] does not seem to immediately extend to listing. We follow an alternative and novel graph-based approach, proposing the first output-sensitive algorithm for this problem: it takes polynomial time in n per MCS found, where n= max { | X| , | Y| } , with polynomial preprocessing time and space.
Enumeration of Maximal Common Subsequences Between Two Strings
Conte A.;Grossi R.;Punzi G.
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2022-01-01
Abstract
A maximal common subsequence (MCS) between two strings X and Y is an inclusion-maximal subsequence of both X and Y. MCSs are a natural generalization of the classical concept of longest common subsequence (LCS), which can be seen as a longest MCS. We study the problem of efficiently listing all the distinct MCSs between two strings. As discussed in the paper, this problem is algorithmically challenging as the same MCS cannot be listed multiple times: for example, dynamic programming [Fraser et al., CPM 1998] incurs in an exponential waste of time, and a recent algorithm for finding an MCS [Sakai, CPM 2018] does not seem to immediately extend to listing. We follow an alternative and novel graph-based approach, proposing the first output-sensitive algorithm for this problem: it takes polynomial time in n per MCS found, where n= max { | X| , | Y| } , with polynomial preprocessing time and space.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
