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RNAstructure is a product of the Mathews Lab, University of Rochester Medical Center, Department of Biochemistry and Biophysics.
Continued development of RNAstructure is made possible by the support of NIH grant R01GM076485.
- AccessFold
- Bimolecular
folding of nucleic acids without intramolecular pairs allowed. This
program uses a heuristic to determine accessibility to to duplex
formation.
- 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).
- design
- Find an RNA (or DNA) sequence that is expected to fold into a given structure.
- 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.
- 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.
- 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).
- 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.
- 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
- 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.
- scorer
- Calculate sensitivity and positive predictive value for two structures being compared.
- ShapeKnots
- Predict a secondary structure that can contains pseudoknots, restrained by SHAPE mapping data.
- stochastic and stochastic-smp
- Generate a representative ensemble of structures.
- TurboFold
- Fold multiple sequences into their optimal conformations, using one of three different folding modes.
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