Developed by genomics researchers at Harvard Medical School, AlignAce employs an algorithm that scans non-coding nucleic acid sequences at high resolution for motifs that occur with non-random frequency. This algorithm is built into a multi-level sequence analysis program that highlights gene-specific regulatory elements for further analysis.

AlignAce offers both efficiency and convenience. Its high signal-to-noise ratio preferentially reduces false positives in the program output, while iterative masking uncovers multiple, distinct sequence motifs within a single data set. In gene expression studies, Alignace easily highlights potential gene regulatory elements and sets of co-regulated genes. Nucleic acid sequences identified by AlignAce may be used as drug targets or, alternatively, as bait to isolate gene-specific trans-regulatory proteins for use as drugs or drug targets.