Revision e176a6609263df6d17f65f3a5bbdd87bebccb48d authored by Ronny Lorenz on 09 April 2016, 16:09:24 UTC, committed by Ronny Lorenz on 21 June 2016, 11:49:15 UTC
- Add packaging/debian/python3-rna.install - Repaired make_windows_installer.sh - Plugged memory leak in RNAcofold - Fixed partition function rescaling bug in RNAup - Fixed bug in RNALfold with window sizes larger than sequence length - Re-added SCI parameter for RNAalifold - Fixed backtracking issue for large G-quadruplexes in RNAalifold - Fixed missing FASTA id in RNAeval output - Added option to RNAalifold that allows to specify prefix for output files - Several fixes and additional functions/methods in scripting language interface(s) - Added version information for scripting language interface(s) - Some changes to allow for compilation with newer compilers, such as gcc 6.1
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NEWS
See Changelog for details.
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.
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