CSC

	Tehdyt toimenpiteet NUCLEIC RNA FOLDING   RNA folding methods and analysis Program name Description ovrnaalifold RNA alignment folding ovrnaalifoldpf RNA alignment folding with partition ovrnacofold RNA cofolding ovrnacofoldconc RNA cofolding with concentrations ovrnacofoldpf RNA cofolding with partitioning ovrnadistance RNA distances ovrnaduplex RNA duplex calculation ovrnaeval RNA eval ovrnaevalpair RNA eval with cofold ovrnafold Calculate secondary structures of RNAs ovrnafoldpf Secondary structures of RNAs with partition ovrnaheat RNA melting ovrnainverse RNA sequences matching a structure ovrnalfold Calculate locally stable secondary structures of RNAs ovrnaplot Plot vrnafold output ovrnasubopt Calculate RNA suboptimals vrna2dfold Structures and samples of k,l neighbourhoods vrnaaliduplex RNA duplex calculation for two sequence alignments vrnaalifold RNA alignment folding vrnaalifoldpf RNA alignment folding with partition vrnacofold RNA cofolding vrnacofoldconc RNA cofolding with concentrations vrnacofoldpf RNA cofolding with partitioning vrnadistance RNA distances vrnaduplex RNA duplex calculation vrnaeval RNA eval vrnaevalpair RNA eval with cofold vrnafold Calculate secondary structures of RNAs vrnafoldpf Secondary structures of RNAs with partition vrnaheat RNA melting vrnainverse RNA sequences matching a structure vrnalalifoldpf Locally stable 2ry structures for a set of aligned RNAs vrnalfold Calculate locally stable secondary structures of RNAs vrnalfoldz Locally stable secondary structures of RNAs plus zscore vrnapkplex RNA structures plus pseudoknots vrnaplfold Locally stable RNA 2ry structures - pair probabilities vrnaplot Plot vrnafold output vrnasubopt Calculate RNA suboptimals