Voting is a software package that discovers common patterns, motif, in a set of DNA sequences. Voting is efficient to solve the planted (l,d) motif problem which discover a hidden length-l string motif appear in each input DNA sequence with at most d Hamming distance. Our package guarantees discovering all motifs in a short time.
Voting software package Released Aug 10,2010
Pevzner and Sze  have introduced the Planted (l,d)-Motif Problem to find similar patterns (motifs) in sequences which represent the promoter region of co-regulated genes. l is the length of the motif and d is the maximum Hamming distance around the similar patterns. Many algorithms have been developed to solve this motif problem. However, these algorithms either have long running times or do not guarantee the motif can be found. In this paper, we introduce new algorithms to solve the motif problem. Our algorithms can find motifs in reasonable time for not only the challenging (9,2), (11,3), (15,5)-motif problems but for even longer motifs, say (20,7), (30,11) and (40,15), which have never been seriously attempted by other researchers because of heavy time and space requirements.
E-mail: Henry C.M. Leung