Chain-RNA is an ncRNA structural alignment program based on extended two-dimensional chain algorithm. It has been applied to pairwise genome-scale ncRNA search.
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IEEE/ACM Trans Comput Biol Bioinform. 2012 Oct 30. [Epub ahead of print]
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorithm.
Lei J, Techa-Angkoon P, Sun Y.