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.
folding of nucleic acids without intramolecular pairs allowed. This
program uses a heuristic to determine accessibility to to duplex
- 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.
two structures for the same sequence, with the nucleic acid backbone
arranged around a circle to facilitate easy comparisons.
- Generate a dot bracket file from a CT file. The CT file can be regenerated from the dot bracket file using dot2ct (below).
- Find an RNA (or DNA) sequence that is expected to fold into a given structure.
- Generate a CT file from a dot bracket file. The dot bracket file can be regenerated from the CT file using ct2dot (above).
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.
- 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.
- 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.
- Generate a free energy dot plot from a folding calculation save file, exported as a Postscript file.
- 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.
- Predict the lowest free energy structure for a nucleic acid sequence, in parallel using a GPU.
- Predict the maximum expected accuracy structure for a nucleic acid sequence.
- Find non-coding RNAs in sequence alignments.
- Find secondary structures common to multiple sequences (more than two).
- Use NMR data to improve the prediction of an RNA secondary structure.
- oligoscreen and oligoscreen-smp
- Determine folding thermodynamics for a set of oligonucleotides.
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.
- Predict nucleic acid base pairing probabilities using a partition function in parallel using a GPU.
a secondary structure common to two nucleic acid sequences, a sample of
those structures, and/or the probability of pairing for common base
- Predict the probablistic alignment between two RNA sequences.
- Generate a base pairing probabilities dot plot from a partition function save file, exported as a Postscript file.
structures from base pair probabilities, using a threshold to include
only pairs within a specific range of probabilities.
- Predict a maximum expected accuracy structure, including pseudoknots.
- Calculate the probabilities of loops or helix stacks.
- Use a save file to predict a new set of suboptimal structures.
- Remove pseudoknots from an RNA structure, outputting the most likely pseudoknot-free structure.
- Calculate sensitivity and positive predictive value for two structures being compared.
- Predict a secondary structure that can contains pseudoknots, restrained by SHAPE mapping data.
- stochastic and stochastic-smp
- Generate a representative ensemble of structures.
- Fold multiple sequences into their optimal conformations, using one of three different folding modes.