Space-Economical Algorithms for Finding Maximal Unique Matches

@inproceedings{Hon2002SpaceEconomicalAF,
  title={Space-Economical Algorithms for Finding Maximal Unique Matches},
  author={Wing-Kai Hon and Kunihiko Sadakane},
  booktitle={CPM},
  year={2002}
}
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: In case 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 log n) and O(n) respectively… CONTINUE READING

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