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Algorithm 1 Algorithm 1 Motif search algorithm

From: Efficient motif finding algorithms for large-alphabet inputs

1. Use multiple rounds of counting sort to iterate over input strings and construct a set of potential motif instances I, k-mers that are at Hamming distance of at most 2m from each string (Algorithm 2).

2. Construct candidate set C by building stem sets H(a, b) for k-mer pairs in I (Algorithm 3)

3. Prune all stems from C that do not satisfy motif property using rounds of counting sort (Algorithm 2, Section ‘Pruning using selection’)

4. Output remaining stems as motifs.