An efficient algorithm for finding short approximate non-tandem repeats

  title={An efficient algorithm for finding short approximate non-tandem repeats},
  author={Ezekiel F. Adebiyi and Tao Jiang and Michael Kaufmann},
  volume={17 Suppl 1},
We study the problem of approximate non-tandem repeat extraction. Given a long subject string S of length N over a finite alphabet Sigma and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact repeats) required by the algorithm, and prove a sublinear bound on their expected numbers. Using this… CONTINUE READING

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