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Algorithm 2 Algorithm 2 Selection algorithm

From: Efficient motif finding algorithms for large-alphabet inputs

Input: set of k-mers with associated sequence index, distance parameter d

Output: set of k-mers at distance d from each input string

   1. Pick d positions and remove from the k-mers symbols at the corresponding positions to obtain a set of (kd)-mers.

   2. Use counting sort to order (lexicographically) the resulting set of (kd)-mers.

   3. Scan the sorted list to create the list of all sequences in which k-mers appear.

   4. Output the k-mers that appear in every input string.