Is there a version of CONTRAlign for aligning DNA sequences?
Currently, there is not. Parameter learning in CONTRAlign relies on the existence of a training set of gold standard alignments. While structural methods are used to obtain gold standard protein sequence alignments, currently no equivalent procedure exists for DNA sequences. We eventually plan to incorporate the unsupervised learning methods used in PROBCONS for nucleotide sequence alignment. Preliminary tests of this strategy using the BRAliBASE 2 RNA alignment benchmark database show that such an approach holds much promise for developing high accuracy alignment algorithms without reference data. Return to top.
