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Hence the maximum time complexity of the algorithm in terms of Big O is NK.
However, due to the exhaustive search the maximum time complexity of the search is within O |Σ*| r ), where Σ* is the compound alphabet and r the maximal allowed motif length.
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However, in practice, due to on-chip memory and decoding complexity constraints, the maximum time interleaving depth is rather small.
Since MMMvII requires exact solutions to these maximum clique subproblems, its worst-case time complexity is exponential.
The best sequential algorithm for the maximum subsequence sum problem, has O(n) time complexity [2].
Listing approximate STRs, however, becomes computationally intractable because its time complexity grows exponentially in the maximum number of allowed mutations (Domanic and Preparata, 2007; Pellegrini et al., 2010).
Huber et al. (2006) fixed an upper bound l on the maximum length of each segment to reduce the time complexity to O(nlS) with l < n.
The time complexity of computing the 1 1 maximum weight bipartite matching is O(m), where m is sum of the cardinalities of A1 and A2.
The time complexity is O Δ3), where Δ is the maximum degree.
All the parameters were kept as default except the maximum number of Epochs was set to 42 to reduce the computational time complexity.
The time complexity of our algorithm matches the fastest known algorithm for the maximum agreement subtree problem for binary trees.
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