Motif Extraction from Weighted Sequences

We present in this paper three algorithms. The first extracts repeated motifs from a weighted sequence. The motifs correspond to words which occur at least q times and with hamming distance e in a weighted sequence with probability ≥ 1/k each time, where k is a small constant. The second algorithm extracts common motifs from a set of N ≥ 2 weighted sequences with hamming distance e. In the second case, the motifs must occur twice with probability ≥ 1/k, in 1 ≤ q ≤ N distinct sequences of the set. The third algorithm extracts maximal pairs from a weighted sequence. A pair in a sequence is the occurrence of the same substring twice. In addition, the algorithms presented in this paper improve slightly on previous work on these problems.