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De novo discovery of over-represented DNA motifs is one of the majorchallenges in computational biology. Although numerous tools have beenavailable for de novo motif discovery, many of these tools are subject to localoptima phenomena, which may hinder detection of multiple distinct motifs. Agreedy algorithm based tool named dMotifGreedy was developed. dMotifGreedybegins by searching for candidate motifs from pair-wise local alignments ofinput sequences and then computes an optimal global solution for each candidatemotif through a greedy algorithm. dMotifGreedy has competitive performance indetecting a true motif and greatly enhanced performance in detecting multipledistinct true motifs. dMotifGreedy is freely available via a stand-aloneprogram at http://lambchop.ads.uga.edu/dmotifgreedy/download.php.

dMotifGreedy: a novel tool for de novo discovery of DNA motifs with enhanced power of reporting distinct motifs