In this paper we propose a new data structure for the efficient extraction of structured motifs from DNA sequences. A structured motif is defined as a collection of highly conserved motifs with pre-specified sizes and spacings between them. The new data structure, called box-link, stores the information on how to jump over the spacings which separate each motif in a structured motif. A factor tree, a variation of a suffix tree, endowed with box-links provide the means for the efficient extraction of structured motifs.
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