Efficient motif finding algorithms for large-alphabet inputs

  title={Efficient motif finding algorithms for large-alphabet inputs},
  author={Pavel P. Kuksa and Vladimir Pavlovic},
  booktitle={BMC Bioinformatics},
We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. The proposed algorithm (1) improves search efficiency compared to existing algorithms, and (2) scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more… CONTINUE READING
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