Abstract
We show space-economical algorithms for finding maximal unique matches (MUM’s) between two strings which are important in large scale genome sequence alignment problems. Our algorithms require only O(n) bits (O(n/ log n) words) where n is the total length of the strings. We propose three algorithms for different inputs: When the input is only the strings, their compressed suffix array, or their compressed suffix tree. Their time complexities are O(n log n), O(n logε n) and O(n) respectively, where ε is any constant between 0 and 1. We also show an algorithm to construct the compressed suffix tree from the compressed suffix array using O(n logε n) time and O(n) bits space.
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Hon, WK., Sadakane, K. (2002). Space-Economical Algorithms for Finding Maximal Unique Matches. In: Apostolico, A., Takeda, M. (eds) Combinatorial Pattern Matching. CPM 2002. Lecture Notes in Computer Science, vol 2373. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45452-7_13
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DOI: https://doi.org/10.1007/3-540-45452-7_13
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