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@martin-raden martin-raden released this 10 Aug 08:06
· 283 commits to master since this release
v3.0.0
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Learn about vigilant mode.

New Features:

  • faster due to seed-extension prediction strategy (--model=X)
  • IntaRNA comes with multiple personalities, i.e. pre-defined parameter sets
    • IntaRNA = IntaRNA3 = default parameters
    • IntaRNAexact : exact prediction (similar to but faster as RNAup)
    • IntaRNAhelix : helix-block-based RNA-RNA interaction prediction
    • IntaRNAduplex : hybrid-only predictions without accessibility consideration
    • IntaRNA1 and IntaRNA2 : emulating prediction behaviour of previous versions
  • ensemble-based RNA-RNA interaction prediction enabled
    • enables the CSV output columns Eall, Zall, P_E that are (for all considered interactions) the overall ensemble energy, overall partition function and the interaction probability for the current interaction (i.e. line)
  • new --mode=S for seed-only predictions
  • CSV output can be sorted by a user-defined column via --outCsvSort=...
  • optional exclusion of lonely base pairs via --outNoLP (not yet implemented for all prediction modi and models but in progress)
  • load pre-set parameters from file via --parameterFile
  • optional exclusion of GU base pairs in seed via --seedNoGU
  • report of all putative seeds (disabled by --outBestSeedOnly) sorted by stability (energy) in detailed output mode
  • highlighting of all seed-covered base pairs in text-based output mode
  • energy computation now integer-based to avoid floating-point-related traceback issues
  • IntaRNA v1 output support not continued

Interface Changes

  • new default value 8 (was 16) for --tIntLoopLen and --qIntLoopLen, which reduces the maximal interior loop length to at most 8 unpaired bases between two base pairs (per RNA)
  • model=B (replaces L) for helix-block-based prediction
  • marker "NAN" for not available values in CSV output
  • in detailed output mode:
    • index ranges without whitespaces, i.e. "1--5" instead of "1 -- 5"
    • gaped loop positions now represented by '-' in

Minor Changes

  • support for multi-precision Z (via GNU quadmath library)

Webserver:

IntaRNA 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)
  • Source Code : archive of the github content for the according version (see help)
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