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The conventional way of identifying DNA motifs, solely based on matchalignment information, is susceptible to a high number of spurious sites. Anovel scoring system has been introduced by taking both match and mismatchalignment information into account. The mismatch alignment information isuseful to remove spurious sites encountered in DNA motif searching. As anexample, a correct TATA box site in Homo sapiens H4/g gene has successfullybeen identified based on match and mismatch alignment information.

Identifying DNA motifs based on match and mismatch alignment information