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NEWS
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Version 2.6.0
-------------
This version introduces modified nucleotides support and a physics-based model to
correct for predictions at non-standard (monovalent) salt concentrations.
At this time we include publically available energy parameters for inosine,
pseudouridine, m6A, 7DA, and purine (a.k.a. nebularine). In addition, we add
stacking parameters for dihydrouridine as predicted by Rosetta/RECESS.
See the Changelog for version 2.6.0 for a complete list of new features and bugfixes.
Version 2.5.0
-------------
The all new release of version 2.5 brings multi-strand interaction prediction! The
new executable tool RNAmultifold is the successor of the RNA-RNA dimer interaction
prediction tool RNAcofold and effectively lifts the restriction to just two interacting
strands. It follows the same principle of concatenating the RNA strands that shall
form a complex and then predicts MFE and partition function. Along with that, it can
also compute equilibrium concentrations of the complexes formed.
See the Changelog for version 2.5.0 for a complete list of additions, novel features
and fixed bugs.
Version 2.4.0
-------------
With version 2.4 sliding-window structure prediction receives the constraint framework!
Starting with this version, the sliding-window secondary structure prediction implementations
as available through RNALfold, RNAplfold, and RNALalifold are constraints-aware. Thus, they
can readily incorporate RNA structure probing data, such as from SHAPE experiments, etc.
See the Changelog for version 2.4.0 for a complete list of new features and bugfixes.
Version 2.3.0
-------------
This version introduces the unstructured domain extension of the RNA folding grammar! This
extension adds RNA-ligand interactions, e.g. RNA-protein, for unpaired stretches in RNA
secondary structures. The feature is easy to use through the command file interface in RNAfold.
See the Changelog for version 2.3.0 for a complete list of new features and bugfixes.
Version 2.2.0
-------------
After almost a year without a new release, we are happy to announce many new features. This
version officially introduces (generic) hard- and soft-constraints for many of the folding
algorithms. Thus, chemical probing constraints, such as derived from SHAPE experiments, can
be easily incorporated into RNAfold, RNAalifold, and RNAsubopt. Furthermore, RNAfold and the
RNAlib interface allow for a simple way to incorporate ligand binding to specific hairpin- or
interior-loop motifs. This version also introduces the new v3.0 API of the RNAlib C-library,
that will eventually replace the current interface in the future.
See the Changelog for version 2.2.0 for a complete list of new features and bugfixes.
Version 2.1.9
-------------
This is a major bugfix release that changes the way how the ViennaRNA Package handles
dangling end and terminal mismatch contributions for exterior-, and multibranch loops. We strongly
recommend upgrading your installation to this or a newer version to obtain predictions that are
better comparable to RNAstructure or UNAFold.
Please see the Changelog for version 2.1.9 for further details on the actual changes to the
underlying energy parameters.
Version 2.1.7
-------------
For a long time, Mac OS X users were not able to correctly build the Perl/Python interface of the
ViennaRNA Package. Starting with v2.1.7, this limitation has been removed, and the interface should
compile and work as expected.
Please see the Install Notes for Mac OS X users for further details.
Version 2.1.0
-------------
Since ViennaRNA Package Version 2.1.0 we have enabled G-Quadruplex prediction support into
RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot.
See the changelog for details.
## Older news
Version 2.0
------------
- Meanwhile, a lot of changes in the RNAlib have accumulated. See the Reference
Manual and the Changelog for further details
- All algorithms use the Turner'04 nearest neighbor model
- The RNAlib provides (OpenMP) threadsafe folding routines per default. This is
enables concurrent calls to the folding routines in parallel. The feature
can be disabled by passing '--disable-openmp' to the configure script
- serious changes in command line parameters. Everything complies with
GNU standard from now on (short options with preceding '-', long options
with preceding '--'.
- FASTA file support for RNAfold. RNA sequences do not need to be passed
on a single line anymore when a FASTA header is provided.
- The new program RNA2Dfold computes MFE, partition function and
stochastically sampled secondary structures in a partitioning of the secondary
structure space according to the base pair distance to two reference structures
- The new program PKplex computes...
- The new program RNALfoldz computes locally stable secondary structures
together with a z-score
- The new program RNALalifold computes locally stable consensus structures for
alignments
- The new program RNAparconv enables the conversion of 'old' energy parameter files
(v1.4-v1.8) to the new format used in version 2.x
Version 1.8
------------
- new RNAalifold has better treatment of gaps and ribosum based covariance
scores. Use the -old switch for compatibility with older RNAalifold
versions.
- RNAplfold -u now computes all accessibilities up to a maximum length
(much faster than computing each individually)
- ATTENTION: output formats of RNAplfold -u and or RNAup have been changed
Programs parsing RNAplfold and RNAup output will have to be modified.
- RNAfold and RNAalifold compute centroid structures when run with -p
use the -MEA option to compute Maximum Expected Accuracy structures.
Version 1.7
------------
- RNAplfold can now be used to compute accessibilities, i.e. the
probability that a stretch of the RNA remains unpaired (and thus
available for intermolecular interactions).
- A new version of RNAup predicts RNA-RNA interactions takeing into account
the competition between inter- and intramolecular structure in both
molcules
- Circular RNAs can be treated by RNAfold, RNAalifold, RNAsubopt, and RNAcofold
- RNAaliduplex predicts RNA-RNA interactions between two sets of aligned
sequences (inter-molecular structure only)
Version 1.6
------------
- The RNAforester program for tree-alignments of RNA structures is now
distributed with the Vienna RNA package, see the RNAforester
subdirectory for more information. RNAforester was written by Matthias
Hoechsmann <mhoechsm@techfak.uni-bielefeld.de>
- The Kinfold program for stochastic simulation of folding trajectories is
now included in the package, see the Kinfold subdirectory.
- cofolding of two structures now supports suboptimal folding and
partition function folding.
ATTENTION: Energies of hybrid structures now include the Duplex-initiation
energy, which was neglected in previous version.
- RNAplfold is a partition function variant of RNALfold. It computes the
mean probability of a (local) base pair averaged over all sequence
windows that contain the pair.
- new utilities to color alignments and consensus structures
- RNAfold -p now computes the centroid structure
- ATTENTION: ensemble diversities in version <1.6.5 are off by a factor 2
Version 1.5pre
-----------
- ViennaRNA now uses autoconfig generated configure scripts for even better
portability (should compile on any UNIX, Linux, MacOS X, Windows with
Cygwin).
- The new RNAalifold program predicts consensus structures for a set of
aligned sequences.
- Complete suboptimal folding is now integrated in the library.
- Beginning support for co-folding of two strands: energy_of_struct() and
RNAeval can now compute energies of duplex structures.
- RNAcofold predicts hybrid structures of two RNA strands
- RNAduplex predicts hybrid structures, while allowing only inter-molecular
base pairs (useful for finding potential binding sites)
- RNALfold predicts locally stable structures in long sequences.
- Major changes to Perl module. See the pod documentation (perldoc RNA).
- RNAsubopt can do stochastic backtracking to produce samples of suboptimal
structures with Boltzmann statistics.
- New utilities to rotate secondary structure plots and annotate them with
reliability data.
- Various small bug fixes
Version 1.4
-----------
- New Turner parameters as described in Mathews et.al. JMB v288, 1999.
Small changes to format of parameter files (old param files won't work!)
- mfe and suboptimal folding will produce only structures without isolated
pairs if noLonelyPairs=1 (-noLP option), for partition function folding
pairs that can only occur as isolated pairs are not formed.
- setting dangles=3 (-d3 option) will allow co-axial stacking of adjacent
helices in mfe folding and energy_of_struct().
Version 1.3.1
-------------
- RNAheat would produce spikes in the specific heat because dangling end
energies did not go smoothly to 0.
- PS dot plots now have an option to use a log scale (edit _dp.ps file
and set logscale to true).
Version 1.3
-----------
- Secondary structure plots now use E. Bruccoleri's naview routines for
layout by default. New utility RNAplot produces secondary structure plots
from structures in bracket notation with several options.
- New -d2 option in RNAfold and RNAeval sets dangles=2, which makes
energy_of_struct() and fold() treat dangling ends as in pf_fold().
-noLP option in RNAfold etc sets noLonelyPairs=1, which avoids most
structures containing lonely base pairs (helices of length 1).
- new utility functions pack_structure() unpack_structure() make_pair_table()
and bp_distance(). RNAdistance adds bp_distance() via -DP switch.
- First release of RNAsubopt for complete suboptimal folding.
- fixed bug in asymmetry penalty for interior loops.
- Default compilation now uses doubles for partition function folding.
Version 1.2.1
-------------
- Fixed bug in version 1.2 of the RNAheat program causing overflow errors
for most input sequences.
- The PS_dot_plot() and PS_rna_plot() routines now return an int. The return
value is 0 if the file could not be written, 1 otherwise.
- This version contains the alpha version of a perl5 module, which let's you
access all the capabilities of the Vienna RNA library from perl scripts.
Version 1.2
-----------
- New energy parameters from (Walter et.al 1994).
- Energy parameters can be read from file.
- RNAeval and energy_of_struct() support logarithmic energy function for
multi-loops.
- gmlRNA() produces secondary structure drawing in gml (Graph Meta Language).
- Many bug fixes.