Vienna RNA News

Important changes between versions

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 no included in the package, see the Kinfold subdirectory.
cofolding of two structures now supports suboptimal folding and partition function folding (still experimental). ATTENTION: Energies of hybrid structures now inlcude 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

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

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().

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).

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.

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.

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.

Updated parameters for both RNA and DNA using the data compiled by David Mathews <David_Mathews@urmc.rochester.edu>.
local versions of RNAalifold a la RNALfold, RNAplfold