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@martin-raden martin-raden released this Mar 2, 2020 · 6 commits to master since this release

IntaRNA

  • BUGFIX: accessibility blocking constraints were only applied to seed location
  • improved Zall estimate (and depending values) for --model=X (default)
  • new arguments:
    • qId|tId : optional id (FASTA prefix) setup for sequence naming
    • acc|accW|accL : meta accessibility setup for both query and target
    • intLenMax|intLoopMax : meta interaction and interior loop length setup

CopomuS

  • Compensatory mutation selector to support interaction validation experiments
Assets 4
Pre-release
  • 3.1.4
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@martin-raden martin-raden released this Jan 31, 2020 · 38 commits to master since this release

IntaRNA

  • bugfix generation and tracing of seeds with bulges and no GU ends (combination of seedNoGUend and seed?MaxUP > 0)
  • bugfix seed-extension prediction for seeds with bulges (seed?MaxUP > 0)
  • outNoLP for seeds with bulges enabled (seed?MaxUP > 0)

auxiliary R scripts

  • IntaRNA_CSV_p-value.R script to estimate p-values based on energy values
  • IntaRNA_plotRegions.R = renaming of former plotRegions.R
Assets 4
  • v3.1.5
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@martin-raden martin-raden released this Jan 31, 2020 · 27 commits to master since this release

IntaRNA :

  • bugfix traceback of interactions with seed on right-boundary
  • bugfix traceback of seeds with bulges when outNoLP present
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  • v3.1.3
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@martin-raden martin-raden released this Nov 4, 2019 · 69 commits to master since this release

Unfortunately, the changes in the latest release v3.1.2 come with a serious traceback bug that is fixed now.

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@martin-raden martin-raden released this Oct 30, 2019 · 76 commits to master since this release

IntaRNA

  • --outSep = user-defined column separator for tabular CSV output
  • bugfix non-overlapping suboptimal enumeration
  • bugfix noLP optimization (missing case of direct left-stack extension)
  • CSV output:
    • new ensemble energy and partition function output for intra-molecular
      structures formed by seq1 and seq2 (Eall1, Eall2, Zall1, Zall2)
    • new total energy output Etotal = (E+Eall1+Eall2) and
      EallTotal = (Eall+Eall1+Eall2)
    • new RT output
    • new bpList output
  • ensemble output:
    • Eall1|2
    • EallTotal
    • RT

auxiliary R scripts

  • R/plotRegions.R - visualization of sequence regions covered by IntaRNA
    predictions, similar to the IntaRNA webserver output (thanks to @dgelsin)

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)
Assets 3
  • v3.1.1
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@martin-raden martin-raden released this Sep 25, 2019 · 101 commits to master since this release

New Features:

IntaRNA

  • predefined parameter sets for loading (Turner04, Turner99, Andronescu07) without providing a respective parameter file from the Vienna RNA package
  • 'tRegion' and 'qRegion' now available for and applied to multi-sequence input
  • base pairs details only computed if needed for output (speedup for large -n)

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)
Assets 3
  • v3.1.0.2
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@martin-raden martin-raden released this Sep 20, 2019 · 114 commits to master since this release

To provide deterministic non-overlapping output, the 'left-most' best interactions are reported. That is, if two non-overlapping interactions have the same next-best energy, the one with lower target or higher query index is selected. That way, output becomes deterministic independently of the operating system and the library versions used to build IntaRNA.

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@martin-raden martin-raden released this Sep 19, 2019 · 116 commits to master since this release

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)
Assets 4
Sep 12, 2019
bugfixes and full v3 features enabled
bugfixes and full v3 features enabled
  • v3.0.0
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@martin-raden martin-raden released this Aug 10, 2019 · 189 commits to master since this release

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)
Assets 4
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