In this paper, an exhaustive algorithm for extracting structured motifs has been presented. Structured motif is
defined as an ordered set of highly-conserved over-presented patterns which occur near each other in a set of DNA
sequences .The presented algorithm is based on an innovative data structure called l-mer trie. As opposed to other
existing motif finders, this algorithm offers more flexibility in terms of the possibility of determining a range for length of
the single patterns, their substitution rates and the spacing between them. The possibility of defining a minimum bound
for substitution rates saves considerable time and space in the case of searching for weak motifs occurring with many
Efficiency of the algorithm has been verified on some artificial sequences as well as real DNA sequences of some plant
viruses. The results have been compared with those achieved by RISO, another tree-based algorithm, which is claimed to
have notable time and space gains over the best known exact algorithms.
Keywords: Exhaustive algorithm, e-mutated set, geminivirideae, l-mer trie, structured motif, tymovirius.
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