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v3.1.0 - bugfix and final v3 features
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@martin-raden martin-raden released this 19 Sep 11:23
· 205 commits to master since this release
v3.1.0.1
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Learn about vigilant mode.

New Features:

IntaRNA

  • overall partitition function estimates Zall and derived output now available for all prediction models
  • ensemble-based prediction revised
  • seed-extension-based prediction revised
  • parse of FASTA input: sequence id = prefix up to first whitespace from FASTA header
  • gzip-compressed file input/output if file name ends in .gz
  • (optional) intarnapvalue python3 module to compute p-values of IntaRNA mfe
    predictions based on sequence shuffling and distribution fitting

Interface Changes

  • new --outMode=E : report of ensemble information only
  • in outMode=D : subsequence range now "START..END" instead of "START--END"
  • new default --outOverlap = B: overlapping output enabled (was Q)
  • --outNoGUend : omit interactions with GU-helix ends
  • --accNoLP : exclude lonely base pair in accessibility computation (energy==V)
  • --accNoGUend : exclude GU-helix ends in accessibility computation (energy==V)
  • --q|tIdxPos0 : user defined sequence indexing for input parsing and output enables
  • --seedNoGUend : prohibit GU base pairs at seed ends
  • --outNoLP support in all prediction modes

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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