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RNA folding is a compute-intensive task that lies at the core of search applications in bioinformatics such as RNAfold and UNAFold. In this work, we analyze the Zuker RNA folding algorithm, which is challenging to accelerate because it is resource intensive and has a large number of variable-length dependencies. We use a technique of Lyngsø to rewrite the recurrence in a form that makes polyhedral analysis more effective and use data pipelining and tiling to generate a hardware-friendlydoi:10.1109/fccm.2010.22 dblp:conf/fccm/JacobBC10 fatcat:kyzf3d7wtjdahgmxvyv5ggxw3m