Abstract:We describe four novel algorithms, RNAhairpin, RNAmloopNum, RNAmloopOrder, and RNAmloopHP, which compute the Boltzmann partition function for global structural constraints-respectively for the number of hairpins, the number of multiloops, maximum order (or depth) of multiloops, and the simultaneous number of hairpins and multiloops. Given an RNA sequence of length n and a user-specified integer 0 £ K £ n, RNAhairpin (resp. RNAmloopNum and RNAmloopOrder) computes the partition functions RNAmloopHP) sample from … Show more
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