Table 1.

DRIMUST – fixed-structure motifs algorithm

Input: A ranked list of sequences A range of motif lengths [k1,k2] P-value threshold for reporting (τ) Output: A list of sequence motifs of lengths between k1 and k2 that are rank imbalanced in at an mHG significance level better than τ. Preprocessing: Construct a generalized suffix tree for such that: All suffixes of all sequences are represented by paths from the root to leaves in the tree. Each leaf contains information about the occurrences of the corresponding suffix w in . This information is represented as a list . The values mi(w) are the indices, amongst , of the sequences at which w occurs. /* The construction is implemented using Ukkonen's algorithm (41) */

Algorithm: for k = k1 to k2 do: Traverse the tree to find paths of length k, and for each path P calculate P's enrichment using the following process: Get the ordered list of indices (ranks) of sequences containing P, extracted from the leaves of the subtree rooted below P. /*P occurs in the union of the lists of all leaves of that subtree, as it is the prefix of all the suffixes represented by these leaves. For example, assuming P appears in S8,S14,S31 and S36, then C = {8,14,31,36} */ Calculate the mHG score for P:   /* Following the example above and assuming we have 100 sequences in the input: In this case attained at i = 4 where */ Report P if holds. /* (20) */