News — ViennaRNA Package

# News

## 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.