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

Genomics