|
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.
- 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.
|
