Identifying DNA motifs based on match and mismatch alignment information
  The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment information into account. The mismatch alignment information is useful to remove spurious sites encountered in DNA motif searching. As an example, a correct TATA box site in Homo sapiens H4/g gene has successfully been identified based on match and mismatch alignment information. 
Jian-Jun Shu and Kian Yan Yong
q-bio.QM q-bio.GN