Skip to content

v2.2.0
Compare
Choose a tag to compare
@martin-raden martin-raden released this 26 Mar 11:38
· 500 commits to master since this release
v2.2.0
151ac9f

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)
Assets 6
Loading