|
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.
- AllSub
-
Generate all suboptimal nucleic acid structures within a small
free energy increment of the lowest free energy structure.
- bifold
-
Bimolecular folding of nucleic acids with intramolecular pairs
allowed.
- bipartition
-
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).
- 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 and dynalign-smp
-
Find a secondary structure common to two sequences. dynalign
finds structures serially, while dynalgn-smp invokes parallel
programming to do so.
- DynalignDotPlot
-
Generate a free energy dot plot from a Dynalign calculation,
exported as a Postscript file.
- efn2 (Energy Function 2)
-
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.
- Fold
-
Predict the lowest free energy structure for a nucleic acid
sequence, as well as a set of low free energy structures.
- MaxExpect
-
Predict the maximum expected accuracy structure for a nucleic
acid sequence.
- NAPSS
-
Use NMR data to improve the prediction of an RNA secondary
structure.
- oligoscreen
-
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
-
Predict nucleic acid base pairing probabilities using a
partition function.
- 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.
- 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.
- 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.
- stochastic
-
Generate a representative ensemble of structures.
| 