CoSTAR: Coarse Stem-Topology Alignment of Pseudoknotted RNA Structures by Relation-Constrained Search (opens in new tab)

RNA structural alignment is a central task in comparative RNA analysis, but many efficient methods achieve tractability by restricting the class of admissible structures, often excluding pseudoknots. This exclusion is limiting for viral and regulatory RNAs, where conserved structure can remain informative even when sequence conservation is weak. We introduce a coarse RNA structural alignment algorithm that aligns secondary structures by searching over partial maps between stems rather than nu...