ACANA (ACcurate ANchoring Alignment)) is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.
Weichun Huang at Biostatistics Branch, the National Institute of Environmental Health Sciences (NIEHS), NIH
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Weichun Huang, David M. Umbach, and Leping Li,
Accurate anchoring alignment of divergent sequences.
Bioinformatics 22:29-34, Jan 1 2006