Abstract:RNA:DNA:DNA triple helix (triplex) formation regulates gene expression, but is difficult to study experimentally in vivo. This makes accurate computational prediction of triplex formation highly important in the field of RNA research. Current predictive methods have used canonical Hoogsteen base pairing rules, which whilst biophysically valid, may not reflect the plastic nature of cell biology. Herein, we present TriplexAligner, a local alignment tool implementing probabilistic scoring matrices learned from tr… Show more
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