RNAstructure 5.8.1 Minor Update (05/30/2016)
- Fixed a bug with the Java GUI on Mac OS X not begin able to set the DATAPATH variable.
- Released a new testing system for the Java GUI.
- Improved regression testing system for RNAstructure programs.
- Example sequences are now mostly FASTA files instead of SEQ.
- Cleaned up whitespace and formatting in several RNA_class source files.
- Java GUI Enhancements:
- Sequence Editor now allows copy/paste and does not restrict keystrokes as before.
Text is color-coded to show invalid bases (red) and lower-case bases (blue) to help highlight potential problems.
- Users can now easily select Recent files or Example files in prediction dialogs
- It is easier to run and monitor multiple concurrent calculations because the
progress indicator is now displayed inside each parameter dialog (instead
of as a separate window disjointed from the main application).
- Some calculations (Fold, AllSub) can now be Canceled.
- Improved "Draw > Go to Structure.." dialog that allows quick an easy scanning through available structures.
- Added new backbone rendering styles for structure drawing: "Render Circular Structure" and "Render Flat (Linear) Structure"
- Improved About Window including function to extract Example files (mostly useful for Mac App Bundle)
- Help menu can directly launch either local or online manual.
- Java GUI now auto-detects the location of data_tables and the native RNAstructure_GUI library, so setting
these on the command-line or environment are no longer necessary. The
jar can be executed directly. The GUI now verifies the version of the
native library to ensure compatibility.
- Fixed detection of operating system to be compatible with newer OS and Java versions.
- Deployment on Mac is now via DMG file for easier installation.
- Fixed a bug that causes zooming issues in the structure drawing window.
RNAstructure 5.8 (12/01/2015)
- Added design
(to find a sequence that will fold to a given structure).
- Added ProbScan
(to calculate loop and stack probabilities).
- Added functionality to draw
to annotate loop probabilities.
- Improved the end-to-end regression testing framework for
- Deprecated the native Windows GUI interface in favor of
the JAVA GUI on all platforms.
a bug where efn2 was incorrectly calculating the average asymmetry for
some multibranch loops. Also, fixed a bug that led to rounding errors.
These changes can also affect Multilign, OligoWalk, and ShapeKnots,
which use efn2.
- Improved the Java GUI behavior when the
native RNAstructure library is not found or cannot be loaded. Now an
error message is shown and the application exits gracefully. Previously
it would crash.
- Improved the Java GUI behavior when the DATAPATH variable is either not set or it
points to an invalid location. Now an informative message is shown at
program startup. Previously no message was shown until the user tried
to perform an action that required native access to the DATAPATH, at which time a less informative message was
- Fixed bugs in the Java GUI:
- Printing structures and images did not work (only blank pages were produced).
GUI would crash on startup if the splash window (or any other program
window) was still open when the main application window was created.
- Typing a non-existant file name in the Open Sequence window caused the program to freeze.
- Selecting a file with an upper- or mixed-case extension resulted in a "File Not Found" error.
- The main menu became unresponsive when the toolbar was moved to a floating window.
- The Java GUI DotPlotDialog window crashed when reading in
postscript legend colors under some circumstances (such as when the
colors were specified as doubles instead of ints (e.g. 10.0 instead of
RNAstructure 5.7 (12/4/2014)1
- Added Dynalign
- Added AccessFold.
- Added phmm,
a pairwise Hidden Markov Model for RNA sequence alignment. This is in
the back ends to Dynalign, Dynalign II, PARTS, and TurboFold. This is a
new front end for sequence alignment.
- Added new help page that provides pathways for using
the command line interfaces.
- Added a flag (--simple) to efn2 so that the energies
can be calculated for structures using the same rules as the dynamic
a bug where specifying a constraint file (in any program or OS) was
removing prior unpairing constraints specified in a sequence file.
a bug in ShapeKnots. While filling in dangle or double mismatches it
created new non-canonical pairs, which led to giving large positive
energies to those structures.
- Improved ShapeKnots speed by removing boundaries
checking in vectors.
- Fixed a bug in the Windows GUI for bimolecular
folding where internal loops were intermittently being forbidden.
the Macintosh compiler flags to match new Clang compiler. Also, revised
code to match the fact that OpenMP is absent from Clang.
RNAstructure 5.6 (7/31/2013)
- Added Multifind to package (Linux and mac only).
parallel processing (SMP) versions of bifold, bipartition, efn2, Fold,
MaxExpect, oligoscreen, partition, and stochastic. These programs take
advantage of multicore computing environments.
Windows GUI now runs in parallel on multicore computers for predicting
lowest free energy structures, calculating partition functions,
calculating free energy changes, oligoscreen calculations, and
- Fixed bug where command line
programs were not recognizing long flags without associated parameters.
This also affected the web servers.
- Fixed a bug with
reading HMM alignment parameters for Dynalign calculations in the
Windows GUI. This was causing the program to crash for Dynalign
- Fixed a bug where bootstraped restraints were not
being correctly calculated in Fold.
RNAstrucure 5.5 Update (5/16/2013)
a new version of the Windows 64-bit graphical interface. This fixes
problems with launching the program from the start menu.
Online Documentation Update (4/16/2013)
- Added instructions for using Windows 8.
RNAstructure 5.5 (4/5/2013)
- Added ShapeKnots as text interface.
- Added GPU version of partition function
(partition-cuda) as text interface.
- Fixed minor memory access issues in NAPSS program.
- Fixed an error in Multilign where SHAPE intercept
and SHAPE slope weren't being set properly.
- Fixed bug in JAVA GUI where opening .seq files from
disk would sometimes fail.
- Updated Makefiles to build more efficiently and
standardized their formats.
- Simplified text interface parsing machinery and
made all flags case-insensitive.
- Cleaned up format, comments, and organization in
all text interfaces that use the standard parsing machinery.
- Updated dnacoaxstack.dat. Fixed problem where a
subset of mismatch-mediated coaxial stacks were missed in DNA.
- Fixed bug where not all special DNA tetraloops
were being read from disk.
- Updated default SHAPE slope and intercept for all
- Changed thresholds for SHAPE color annotations.
- Added support for knowledge-based free energy
terms for stacking restraints in Fold.
- Reduced the size of dot plot labels so they
didn't run together in certain instances.
- Made a small change to dot plot layout so dots at
the first nucleotide index always fall on the first grid line.
- Fixed a bug where sometimes plot bounds weren't
set right, so some dots weren't shown.
- Fixed a bug where sometimes the drawing windows
wouldn't resize properly when dragged.
- Added the ability to draw structures with their
backbone stretched out in a straight line.
- Improved drawing of structures so large
structures are drawn faster, and move and zoom more efficiently.
a glitch in CircleCompare where sometimes the probability annotation
for the accepted structure was being shown for all structures, not for
each predicted structure.
- Fixed a glitch in CircleCompare where probability
annotation was not always consistent in pairs.
- Added distinct flags to CircleCompare so the user
can annotation with either predicted or accepted structure
the ability for structure drawing programs to read probability
information from dot plot text files as -log10(Probability).
- Added the ability for ProbabilityPlot to read dot
data from a standard dot plot file.
mistake in TurboFold documentation where the SHAPEslope and
SHAPEintercept default values were reversed. This reversal was only in
Windows Text Interface Executables Update
for RNAstructure 5.4 (09/05/2012)
a new version of .zip files (both 32- and 64-bit), which fixes an error
with ProbabilityPlot, EnergyPlot, and DynalignDotPlot where these
programs would not work on all Windows Computers.
Web Servers (08/28/2012)
- Improved CT file reading by making it more robust to
differences in format.
Mac OS X Executables Update for
RNAstructure 5.4 (08/23/2012)
- Fixed a bug where the Java GUI didn't always run
properly. Current executables run on Snow Leopard, Lion, and Mountain
Web Servers (08/13/2012)
- Fixed bug where pasted sequences without new lines at
the end sometimes caused calculation errors.
Web Servers (08/10/2012)
- Fixed bug in multiple sequence servers where a FASTA
file wasn't being uploaded and split into multiple sequences properly.
- Changed wall time of run scripts from one hour to one
Web Servers (08/09/2012)
- Clarified error message that occurs when no sequence
input at all is given to a web server that takes sequence input.
a bug in the Predict a Secondary Structure server where the calculated
partition function save file wasn't being used for all calculations.
a bug in the Multilign and TurboFold servers where the proper error
page wasn't being shown if too few or too many sequences were given.
Web Servers (08/08/2012)
- Fixed broken links and style sheet references on page
that shows up if structures have no pairs.
RNAstructure 5.4 (08/02/2012)
- Added webservers for all programs.
- TurboKnot added to GUI as an option in TurboFold.
- Breakage of DNA pseudoknots, as well as pseudoknot
breakage options, added to JAVA GUI.
- Added 64-bit executables as downloads for Windows.
Windows GUI to conform with Windows 7 standards. This also fixes issues
with drawing dot plots from text files and issues with showing
oligonucleotide self-structure from the OligoWalk interface.
- Fixed a bug in the Windows GUI, where pressing the F1
key resulted in a "Failed to Launch Help" window in Windows XP and
command line bug in bifold interface where the intramolecular flag did
not always forbid intramolecular pairs as it should have.
command line bug in text interfaces where whole numbers specified with
zeros after a decimal point were sometimes rejected as non-numeric.
Negative numbers were also sometimes rejected as non-numeric.
the documentation for the Dynalign text interface, where the default
"DNA = false" should have been written as "DNA = 0." Also, to set DNA
folding, the user should specify "DNA = 1."
- Fixed a
typo in miscloop.dat and dnamiscloop.dat tables in data_tables
directory. The file stated "miscloop asym," but now states "multiloop
asym." This value is the multibranch loop asymmetry penalty that is
used by efn2. This did not affect structure prediction or energy
calculations, and the change was made to simply clarify what
thermodynamic parameter this is.
- Corrected bug in
JAVA GUI where the partition function bimolecular module sometimes
overwrote its second input sequence file, rather than using the desired
- Corrected bug in JAVA GUI where file chooser
extension sanity checks sometimes failed.
- Added an RNAstructure_java_utilities folder to
facilitate expansions in JAVA capabilities.
- Re-implemented internal workings of the JAVA GUI to
aid in organization and comprehension.
- Fixed a bug in Dynalign, where conserved 3' dangling
ends on helices at exterior loops were not allowed.
- Fixed a bug in extrapolation of free energies to
temperatures other than 37 degrees C.
- Fixed a dot plots bug where dots at the boundaries of
color ranges sometimes showed up as the wrong color or disappeared.
- Reorganized Makefiles to build more efficiently and
include explicit dependencies.
- Standardized Postscript and SVG structure drawing so
their default is always clockwise orientation.
a redone JAVA drawing framework, which includes the ability to create
self-contained JAVA drawing programs for structures and dot plots.
- Simplified the controls in the JAVA drawing framework
so only the structure currently drawn can be exported to Postscript.
items where necessary to the JAVA drawing framework so structures and
dot plots can be exported as both Postscript and SVG.
- Fixed a bug in JAVA drawing framework where the
default for structures wasn't clockwise orientation.
- Removed "New Window" and "Arrange Icons" options,
which did nothing, from the menus of the Windows GUI.
ability to switch between structures and zoom in the drawing framework
using the command key (on Mac) as well as the control key.
- Fixed the description of MAP mode in the PARTS text
RNAstructure 5.3 (05/10/2011)
- Added TurboFold to the package.
- Fixed a bug where drawing suboptimal structures did
not always work in the JAVA GUI for Mac and Linux.
a bug where bimolecular partition functions were missing some states
(single dangling ends and no dangling ends) at helix ends.
- Added the ability to include SHAPE data when
calculating folding free energy changes with efn2 program.
- Added the ability to apply folding restraints for the
formation of specified base pairs.
Windows and JAVA graphical interfaces for OligoWalk to show the correct
temperature of folding free energy changes when a user adjusts the
temperature of the calculation. (Prior to this, free energies' changes
were always listed as being at 37 degrees C.)
- Added the Overview help pages to the manual.
bug in JAVA GUI where the message bar at the bottom of the screen
didn't always update when a temperature menu was clicked.
bug in JAVA GUI in OligoScreen where file names were being refreshed
incorrectly. Also switched oligomer type default to DNA, rather than
- Corrected bug in JAVA GUI of OligoWalk where
oligonucleotides were always RNA, even when DNA was selected.
RNAstructure 5.2 (11/17/2010)
- Added Multilign to the package.
an issue when breaking pseudoknots, but leaving the maximum
non-pseudoknotted pairs, where non-canonical pairs in the input
structure were mistakenly broken. This was also an issue with the count
of pseudoknotted pairs in the CircleCompare program.
- Added support for writing ct files for long sequences
- Removed GAIL rule from dnamiscloop.dat and
the internal loop asymmetry penalty a single constant for DNA folding.
This fixed an occassional bug with folding by DNA rules.
- In Windows GUI only, changed default value for the
minimum helix length in ProbKnot from 2 to 3, which is the preferred
- Added color-annotation for single-stranded
nucleotides in drawing programs.
- Added the ability to use DNA parameters to the
Dynalign command line interface.
- Added the ability to change the folding temperature
in the Dynalign command line interface.
- In the Windows GUI, set the default file choice to
.ALI when clicking the "Alignment File" button.
Dynalign, revised the model for using alignment data to limit the
extent of calculation. This can lead to a different set of suboptimal
structures than previous versions. This also fixes a traceback error
encountered in rare circumstances.
- Added the EnsembleEnergy program to the command line
- Improved the font in the html help for the GUI.
RNAstructure 5.1 (06/30/2010)
the thermodynamic parameter for adding an additional helix to a
multibranch loop ("helix penalty" in miscloop.dat). The value is now
set to -0.6 kcal/mol, which is the value determined by a linear
regression fit to experimental data. This value provides slighly higher
average accuracy for maximum expected accuracy structure prediction
(MaxExpect and ProbKnot programs). This change means that predicted
structures might be different than those predicted by previous version
of RNAstructure. Base pair probabilities, however, should be highly
similar to predictions from previous versions of the program.
- Added ProbKnot program to text interfaces and GUIs.
- Added online help for text (command line interfaces).
- Restructured downloads so that the text interface
binaries now also come with complete repository, including help and
- Added circular drawings to GUIs for drawing
structures that contain pseudoknots.
- Added the ability to read FASTA-formatted sequence
- Updated online help for GUIs to better reflect the
current state of the software.
- Fixed problems with Dynalign dot plots.
- Fixed problem reading SHAPE data in JAVA GUI.
RNAstructure 5.03 (03/22/2010)
the automatic generation of a title for new sequences in the GUIs (both
Windows and JAVA). This fixes a problem where RNAstructure fails to
recognize a sequence because it contained no title.
- Added CircleCompare (comparision of two secondary
structures, including pseudoknots).
- Fixed the grayed "forbid unimolecular pairs" menu
option when performing bimolecular folding with the Windows GUI.
RNAstructure 5.02 (01/22/2010)
- Revised PARTS to make it more user friendly.
- Fixed problem where precompiled text interfaces could
not find the shared library on some machines and therefore not run.
RNAstructure 5.01 (12/30/2009)
- Added the ability to read FASTA-formatted sequences
to text interfaces.
- Added the Dynalign Intel C++ project for Microsoft
Visual Studio to download.
- Added the Fold Intel C++ project for Microsoft Visual
Studio to download.
- Changed the default parameters for SHAPE data pseudo
energies to match best practices.
- Cosmetic changes made to a number of the text
- Fixed a problem where text interfaces on Linux and
Mac could not find the shared library and therefore did not run.
New major update of RNAstructure. This version has a graphical user
interface in JAVA for use on Mac and Linux machines. Text interfaces
are now available for DOS, Linux, and Mac OS X. A class library is
available for programmers. All source code is available for download.
New Windows text interface binaries posted. This fixes the problem that
manifests with the error "This application has failed to start because
the application configuration is incorrect," which appeared on some