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Motif Extraction from Weighted Sequences
 Proc. 11th Symposium on String Processing and Information Retrieval (SPIRE), volume 3246 of LNCS
, 2004
"... 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 algori ..."
Abstract

Cited by 3 (2 self)
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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 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.
www.elsevier.com/locate/tcs Longest repeats with a block of k don’t cares
, 2006
"... A krepeat is a string wk = u ∗ k v that matches more than one substring of x, where ∗ is the don’t care letter and k> 0. We propose an O(n log n)time algorithm for computing all longest krepeats in a given string x = x[1..n]. The proposed algorithm uses suffix trees to fulfill this task and relie ..."
Abstract
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A krepeat is a string wk = u ∗ k v that matches more than one substring of x, where ∗ is the don’t care letter and k> 0. We propose an O(n log n)time algorithm for computing all longest krepeats in a given string x = x[1..n]. The proposed algorithm uses suffix trees to fulfill this task and relies on the ability to answer lowest common ancestor queries in constant time. © 2006 Elsevier B.V. All rights reserved.