RNAstructure 6.0.1 Minor Update (02/12/2018)
- Improved GUI regression testing.
- Fixed a bug in the Java GUI that prevented the Stochastic and OligoWalk tools from running when START was clicked.
- Fixed a minor bug in the energy calculation of flush coaxial stacking in exerior loops (ergexterior). The bug caused very small energy differences in rare circumstances.
RNAstructure 6.0 (09/21/2017)
- Calculations are now performed in "parallel mode" -- i.e.
threads. (This was also true of the previous
native Windows Interface, but not the Java Interface.)
- Improved Sequence "Speak" sound files (• Removed
clicks and gaps at beginning and end of files • Increased
shorter sounds • Added alert sound for invalid characters •
beginning of "C" to sound less like "T")
- Added new menu "Structure Prediction" that combines several
structure analysis workflows for predicting single structures,
bimolecular structures, and structures common to two or more
- StructureEditor added. This JAVA program
edits structure drawings and outputs publication-quality
drawings. This also can edit the underlying base pairing
structure and sequence.
Version 5.8.1 (Released 06/06/2016)
- Fixed a bug with the Java GUI on Mac OS X not begin able to
set the DATAPATH variable.
- 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
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)
- 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
jar can be executed directly. The GUI now verifies the version
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
- Fixed a bug that causes zooming issues in the structure
- Example sequences are now mostly FASTA files instead of
- Released a new testing system for the Java GUI.
Version 5.8 (Released 12/01/2015)
Windows native version is now deprecated. From now on, only
version will be used on all platforms to reduce overhead.
- Improved the Java GUI behavior when the
native RNAstructure library is not found or cannot be loaded.
error message is shown and the application exits gracefully.
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
program startup. Previously no message was shown until the
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
window) was still open when the main application window was
- 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
postscript legend colors under some circumstances (such as
colors were specified as doubles instead of ints (e.g. 10.0
Version 5.7 (Released 12/4/2014)
- Fixed a bug in the Windows GUI for bimolecular folding where
internal loops were intermittently being forbidden.
Version 5.6 (Released 7/31/2013)
Windows GUI now runs in parallel on multicore computers for
lowest free energy structures, calculating partition
calculating free energy changes, oligoscreen calculations, and
- Fixed a bug with reading HMM
alignment parameters for Dynalign calculations in the Windows
was causing the program to crash for Dynalign calculations.
Version 5.5 (Released 4/5/2013)
- Fixed bug in JAVA GUI where opening .seq files from disk
would sometimes fail.
Version 5.4 (Released 8/2/2012)
- Added TurboKnot function to TurboFold module.
- JAVA GUI overhauled to appear more native-like on Mac and
- Windows GUI updated to Windows 7 standards.
- Breaking DNA pseudoknots added to JAVA GUI.
- Removed "New Window" and "Arrange Icons" options, which did
nothing, from the menus of the Windows GUI.
bug in JAVA GUI where the partition function bimolecular
sometimes overwrote its second input sequence file, rather
the desired output name.
- Corrected bug in JAVA GUI where file chooser extension
sanity checks sometimes failed.
- Fixed a bug in the Windows GUI, where pressing the F1 key
resulted in a "Failed to Launch Help" window in Windows XP and
Version 5.3 (Released 5/10/2011)
- Added TurboFold module for RNA folding.
- Fixed bug in JAVA version that occassionally prevented
drawing of suboptimal structures.
a bug where bimolecular partition functions were missing some
(single dangling ends and no dangling ends) at helix ends.
- Fixed bug in JAVA version that caused OligoWalk energy
values to sometimes be displayed incorrectly.
bug in partition function calculations when SHAPE data are
the precision of the SHAPE pseudo free energy changes was
OligoWalk to show the correct temperature of folding free
changes when user adjusts the temperature of the calculation.
this, free energy changes were always listed as being at 37
bug in JAVA version where the message bar at the bottom of the
didn't always update when a temperature menu was clicked.
bug in JAVA version in OligoScreen where file names were being
refreshed incorrectly. Also switched oligomer type default to
rather than RNA.
- Corrected bug in JAVA version of OligoWalk where
oligonucleotides were always RNA, even when DNA was selected.
Version 5.2 (Released 11/17/2010)
- Added Multilign to interface.
- Added color annotation for single-stranded nucleotides. See
the draw help page.
- Added support for writing ct files for long sequences
- Removed GAIL rule from dnamiscloop.dat and dnamiscloop.dh.
- Made the internal loop asymmetry penalty a single constant
for DNA folding.
- On Windows only, changed the minimum helix length in
ProbKnot from 2 to 3, which is the preferred value.
- On Windows only, fixed the Dynalign "Alignment File" button
to display .ALI files by default.
Dynalign, revised the model for using alignment data to limit
extent of calculation. This can lead to a different set of
structures than previous versions. This also fixes a traceback
encountered in rare circumstances.
- Improved the fonts in this online manual so that text
appears better on Windows.
Version 5.1 (Released 6/30/2010)
RNA free energy parameter for adding additional helices to a
multibranch loop was changed from -0.9 to -0.6 kcal/mol. This
that found by linear regression to experimental data. The -0.6
value results in higher average accuracy when using the
expected accuracy methods, MEA and ProbKnot. Note that this
predicted structures may not be identical to those predicted
versions of the software.
- Menu item names harmonized between Windows GUI and JAVA GUI.
- Circular drawings for structures with pseudoknots added to
- Improved online help.
- Fixed a glutch in JAVA version where SHAPE files could not
be read from disk.
- Added the ability to read FASTA-formatted sequence files.
Version 5.03 (Released 3/22/2010)
- Fixed glitch where failure to enter a title in the New
Sequence window resulted in invalid sequence files.
Version 5.02 (Released 1/22/2010)
- No changes to the GUI.
Version 5.01 (Released 12/30/2009)
- Changed the default parameters for SHAPE data pseudo free
energy changes to match best practices.
Version 5.0 (Released 9/30/2009)
- Program is now portable across multiple operating systems.
- Created "RNA" and "DNA" menus to aim specific calculations
at particular nucleic acid types.
option box which allowed the user to write thermodynamic
for Energy Function 2 (Efn2) was non-functional in version
has been corrected.
- Standardized viewing options for drawing and zooming
structures and dot plots.
Version 4.6 (Released 5/5/2008)
- Added the ability to specify SHAPE data for RNA Fold Single
- Added stochastic sampling.
Version 4.5 (Released 4/9/2007)
- Added the capability to specify the maximum distance between
- Added HMM alignment method to limit Dynalign's search space
in the alignment domain.
Version 4.4 (released 8/17/2006)
- Generate All Suboptimal Structures module added.
- Secondary structures can now be predicted at temperatures
other than 37 degrees Celsius.
- Some menu options in force were grayed out and
non-functional in 4.3. This has been corrected.
free energy table for multibranch loops used by Dynalign
(dynalignmiscloop.dat) incorrectly used an older set of
This has been corrected. (Note that this was not the case for
source code version of Dynalign, so the two versions are now
Version 4.3 (released 3/16/2006)
- Base pair probabilities, as determined by the partition
function calculation, can now be output to a text file.
is greatly accelerated by not considering base pairs that are
determined by single sequence secondary structure prediction
occur in structures with relatively high folding free energy
Dynalign is also accelerated by redefining the M parameter
the alignments that are considered. A much smaller M can now
[Note that as of RNAstructure 4.5, the use of M is