v2.2.1

Bugfix release

• fixes compilation issue with ViennaRNA API
• fixes output issues in multi-threading mode
• version output extended (with version of used ViennaRNA and boost library)

v2.2.0

New Features:

• it is now possible to incorporate SHAPE reactivity/structure probing data if available
• out mode spotProb : tracks for a given set of interaction spots their probability to be covered/spanned by an interaction. Furthermore, the probability that none of the spots of interest is covered is provided.
• --qSet/--tSet : parameter to define sequence subset to be considered for prediction (thanks to Alex Gawronski)
• accessibility constraint extended (now specification of 'paired' positions possible as well as short range-based encodings)
• --qRegionLenMax/--tRegionLenMax: automatically identifies highly accessible regions of the sequence and provides list of according intervals where each is below a given threshold in length (also lower bound provided). This is done by iteratively identifying the max ED window (of given size) within too long ranges and removing it, which results either in a shrink of the range or a decomposition into two ranges. This is repeated until all ranges are sufficiently short. (thanks to Alex Gawronski)
• --threads=0 parallelizes on all available cores
• --outPerRegion : individual interaction predictions for all specified regions

Bugfixes:

• accessibility constraint checks were applied to whole regions rather than interval ends
• better floating point number equality checks
• bugfix of predictor handling of accessibility constraints

General:

• dependency update: ViennaRNA version >= 2.4.4 to enable extended and bugfixed VRNA-API
• log-file handling: it is now possible to define where all informative output is written to
• configure : --enable-static-linking flag added to build statically linked binaries; silent make output enabled
• parallelization extended

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• intaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin using VRNA 2.4.4)
• intaRNA-VERSION-API.zip : documentation of the IntaRNA C++ library in html format (see help)
• intaRNA-VERSION-API.pdf : documentation of the IntaRNA C++ library in pdf format (see help)
• Source Code : archive of the github content for the according version (see help)

v2.1.0

Feature and bugfix release.

New Features:

• it is now possible to provide explicit seed input if initial interaction details are known or to be enforced
• dependency update: ViennaRNA version >= 2.4.1 to enable extended VRNA-API
• colored log output now optional (can be disabled via configure script)
• uses now recent easylogging++ version 9.95

Bugfixes:

• integration of blocked accessibility constraints corrected
• Nussinov-like accessibility computation corrected (thanks @sjannielefevre for bringing this up)

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• intaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support using VRNA 2.4.1)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin using VRNA 2.4.1)
• intaRNA-VERSION-API.zip : documentation of the IntaRNA C++ library in html format (see help)
• intaRNA-VERSION-API.pdf : documentation of the IntaRNA C++ library in pdf format (see help)
• Source Code : archive of the github content for the according version (see help)

v2.0.5

Minor bugfix release.

Bugfixes:

• minimal energy profile output for predictions enforcing a seed were wrongly including both interactions with and without seeds
• multi-prediction output for exact mode was crashing (thanks to Rick Gelhausen)

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• intaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support using VRNA 2.3.1)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin using VRNA 2.3.3)
• intaRNA-VERSION-API.zip : documentation of the IntaRNA C++ library in html format (see help)
• intaRNA-VERSION-API.pdf : documentation of the IntaRNA C++ library in pdf format (see help)
• Source Code : archive of the github content for the according version (see help)

v2.0.4

Minor bugfix release.

New features:

• normalized energy output now available in CSV output = E / ln( length1*length2 )
• hybridization energy output now available in CSV output = E - ED1 - ED2
• normalized hybridization output now available in CSV output
• extended description of library usage (easylogging++ initialization) (thanks to Maria Waldl)

Bugfixes:

• file naming and path handling in multi-file output fixed (thanks to Milad Miladi)
• shebang of perl interfaces corrected (thanks to Patrick Wright)

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• intaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support using VRNA 2.3.1)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin using VRNA 2.3.3)
• intaRNA-VERSION-API.zip : documentation of the IntaRNA C++ library in html format (see help)
• intaRNA-VERSION-API.pdf : documentation of the IntaRNA C++ library in pdf format (see help)
• Source Code : archive of the github content for the according version (see help)

v2.0.3

Minor bugfix release.

New features:

• Accessibility computation for Nussinov-Jacobson base pair maximization model (thanks to Mostafa Mahmoud)
• OS X installation instructions using homebrew (thanks to Lars Barquist)

Bugfixes:

• reinitialization incomplete when multiple target/query regions specified (thanks to Alex Gawronski)
• configure script corrected (pkgconfig checks and doxygen setup)
• not all documentation sources part of the downloadable source package

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• intaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support using VRNA 2.3.1)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin using VRNA 2.3.3)
• intaRNA-VERSION-API.zip : documentation of the IntaRNA C++ library in html format (see help)
• intaRNA-VERSION-API.pdf : documentation of the IntaRNA C++ library in pdf format (see help)
• Source Code : archive of the github content for the according version (see help)

v2.0.2

Minor bugfix and source reorganization release.

New features:

• core classes and functionality is now available as a C++ library with IntaRNA namespace (see help)

Bugfixes:

• multi-region definition was resulting in incomplete data structure reinit in heuristic prediction mode
• seed traceback was not using correct offsets if prediction regions are constrained

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• IntaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin)
• IntaRNA-VERSION-API.tar.gz : documentation of the IntaRNA C++ library (see help)
• Source Code : archive of the github content for the according version (see help)

v2.0.1

A minor bugfix and feature release covering:

Interface changes:

• minor documentation errors in the IntaRNA command line interface
• altered output file command line interface (all set via --out= argument instead of individual arguments)

New features:

• support for accessibility in/output for multi-sequence FASTA input
• support for position-wise minimal energy profile output (per sequence)
• support for intermolecular index pair-wise minimal energy output (per query-target sequence pair)

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads (see installation guide):

• IntaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support)
• IntaRNA-VERSION-windows-64bit.zip : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin)
• Source Code : archive of the github content for the according version (see help)

v2.0.0

IntaRNA 2.0.0

This is a major release of the IntaRNA package that partially breaks backward compatibility.

We have thoroughly and completely recoded IntaRNA to enable

• various energy parameter sets (derived from Vienna RNA package)
• modularized prediction modes (heuristic, exact, with and without seed constraints, ..)
• flexible output (CSV, ASCII chart, interaction details, ..)
• customizable accessibility setup (VRNA-based computation, load of precomputed unpaired probabilities, ..)
• multi-threading

... and many other features.

For a complete list and extensive documentation see the IntaRNA main page.

For backward compatibility according input wrappers (perl scripts) and output modes are provided.

Webserver:

The recent IntaRNA version is also available for ad hoc use (with limited parameterization but extended input/output features) at the Freiburg RNA tools webserver.

Downloads:

• IntaRNA-VERSION.tar.gz : source code distribution (see help)
• IntaRNA-VERSION-linux-64bit : statically precompiled binary for linux/unix 64bit (without multi-threading support)
• IntaRNA-VERSION-windows-64bit : precompiled binary and required libraries for MS Windows 64bit (built on Win7pro with Cygwin)
• Source Code : archive of the github content for the according version (see help)

Initial Github release

1.2.5

Add travis build status