| ## RNAstructure Command Line Help Version 6.6 | ### Contents ### Index
RNAstructure is a product of the Mathews Lab, University of Rochester Medical Center, Department of Biochemistry and Biophysics, with the help of many contributors. Continued development of RNAstructure is made possible by the support of NIH grant R35GM132185. ### General Help Instructions for building the text interfaces General instructions for specifying thermodynamic parameters I/O file formats Common pathways for analysis, i.e. how the programs work together A list of available thermodynamic parameters and folding alphabets ### Specific Interface Help AccessFold Bimolecular folding of nucleic acids without intramolecular pairs allowed. This program uses a heuristic to determine accessibility to to duplex formation. AlignmentFold Predict the conserved consensus structure for a set of aligned homologous sequences. AlignmentPartition Predict base pairing probabilities for consensus structures using a partition function. AllSub Generate all suboptimal nucleic acid structures within a small free energy increment of the lowest free energy structure. bifold and bifold-smp Bimolecular folding of nucleic acids with intramolecular pairs allowed. bipartition and bipartition-smp Bimolecular partition function calculation of nucleic acids without intramolecular pairs allowed. CircleCompare Compare two structures for the same sequence, with the nucleic acid backbone arranged around a circle to facilitate easy comparisons. ct2dot Generate a dot bracket file from a CT file. The CT file can be regenerated from the dot bracket file using dot2ct (below). CycleFold Predict canonical and non-canonical base pairs. DecoyFinder Identify sequences that are not homologous with others in a set of sequences. design and design-smp Find an RNA (or DNA) sequence that is expected to fold into a given structure. Diana_Cluster.R Cluster structures in a CT file and write the cluster centroids. dot2ct Generate a CT file from a dot bracket file. The dot bracket file can be regenerated from the CT file using ct2dot (above). draw Draw a structure (or structures) in Postscript from a CT file. This can be done a variety of ways: annotated, unannotated, circularized, or a combination of these. DuplexFold Bimolecular folding of nucleic acids without intramolecular pairs allowed. dynalign_ii, dynalign, dynalign_ii-smp, and dynalign-smp Find a secondary structure common to two sequences. DynalignDotPlot Generate a free energy dot plot from a Dynalign calculation, exported as a Postscript file. EDcalculator and EDcalculator-smp Determine the Ensemble Defect of a structure (compared to the ensemble of all possible structures). efn2 (Energy Function 2) and efn2-smp Determine the folding free energy change of a structure. EnergyPlot Generate a free energy dot plot from a folding calculation save file, exported as a Postscript file. EnsembleEnergy Calculate the ensemble energy of structures from base pair probabilities or sequence data. ETEcalculator and ETEcalculator-smp Estimate the end-to-end (ETE) distance of a sequence in nm. Fold and Fold-smp Predict the lowest free energy structure for a nucleic acid sequence, as well as a set of low free energy structures. Fold-cuda Predict the lowest free energy structure for a nucleic acid sequence, in parallel using a GPU. MaxExpect Predict the maximum expected accuracy structure for a nucleic acid sequence. Multifind Find non-coding RNAs in sequence alignments. multilign Find secondary structures common to multiple sequences (more than two). mutate2test Design disrupting and restoring mutations to test a model secondary structure. (Located in RNAstructure/scripts .) NAPSS Use NMR data to improve the prediction of an RNA secondary structure. oligoscreen and oligoscreen-smp Determine folding thermodynamics for a set of oligonucleotides. OligoWalk Calculate thermodynamic features of sense-antisense hybridization and predict free energy changes of oligonucleotides binding to target RNA. orega (Optimize RNA Ends with a Genetic Algorithm) Use a genetic algorithm to evolve a sequence to change the end-to-end distance. partition and partition-smp Predict nucleic acid base pairing probabilities using a partition function. partition-cuda Predict nucleic acid base pairing probabilities using a partition function in parallel using a GPU. PARTS Find a secondary structure common to two nucleic acid sequences, a sample of those structures, and/or the probability of pairing for common base pairs. phmm Predict the probablistic alignment between two RNA sequences. ProbabilityPlot Generate a base pairing probabilities dot plot from a partition function save file, exported as a Postscript file. ProbablePair Predict structures from base pair probabilities, using a threshold to include only pairs within a specific range of probabilities. ProbKnot (encompasses ThreshKnot) Predict a maximum expected accuracy structure, including pseudoknots. ProbScan Calculate the probabilities of loops or helix stacks. refold Use a save file to predict a new set of suboptimal structures. RemovePseudoknots Remove pseudoknots from an RNA structure, outputting the most likely pseudoknot-free structure. Rsample Uses SHAPE mapping data to output a partition function save file, which can be used to model the structure of a sequence that populates multiple conformations. scorer Calculate sensitivity and positive predictive value for two structures being compared. Shannon Calculate the base pairing Shannon entropy per nucleotide in a sequence. ShapeKnots Predict a secondary structure that can contains pseudoknots, restrained by SHAPE mapping data. stochastic and stochastic-smp Generate a representative ensemble of structures. SymmetryTester Test the required symmetries in a set of data tables. TurboFold Fold multiple sequences into their optimal conformations, using one of three different folding modes. TurboHomology Predict a secondary structure by homology modeling when there is an alignment of homologs with know structure.