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Releases: BackofenLab/IntaRNA

3.3.2 - bugfix IntaRNAhelix

13 Sep 11:31
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IntaRNA

  • compilation fix: correcting shared variables for parallelization
  • BUGFIX debug check
  • BUGFIX IntaRNAhelix traceback of helices where seed is not at right end

3.3.1 - bugfix FASTA parsing

28 Mar 09:12
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IntaRNA

  • BUGFIX: empty lines with white spaces within FASTA input were causing parsing
    errors

3.3.0 - pairwise sequence processing

15 Feb 08:42
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IntaRNA

  • --outPairwise enables pairwise sequence processing instead of all-vs-all
  • input range for --q|tIdxPos0 is now +-2,000,000,000 (was +-9,999,999) to enable genomic position settings

3.2.2 - bugfix release

10 Jan 17:13
c7b50f5
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IntaRNA

  • BUGFIX: maximal interaction length correction for precomputed accessibility
    data was one to large (wrong dangling end computation for maximally long RRIs)
    (thanks to Sabine Reisser)
  • BUGFIX: explicit seed encodings within last 7 nucleotides (seedBP) were
    ignored (thanks to Sebastian Holler)
  • BUGFIX: outNoLP option was not correctly implemented (missing recursion cases)
    and was thus missing interactions
  • BUGFIX: osx: configure adaptation to old grep version in osx

3.2.1 - bugfix release

27 Nov 12:28
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IntaRNA

  • support for multi-seq input when seedQ|TRange given
  • BUGFIX: Andronescu07 energy parameter set was not loaded by name without file
  • BUGFIX: outMinPu was not fully implemented
  • BUILDFIX: non-global import of boost::bind to avoid warnings/problems with recent boost library version

CopomuS :

  • exit value 0 if no favorable interaction was found

3.2.0 - CopomuS + fixed accessibility constraints

02 Mar 09:19
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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

3.1.5 - bugfix bulged seeds with noLP

31 Jan 20:10
cee06fc
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IntaRNA :

  • bugfix traceback of interactions with seed on right-boundary
  • bugfix traceback of seeds with bulges when outNoLP present

3.1.4 - bugfix and extend bulged seed handling + `IntaRNA_CSV_p-value.R`

31 Jan 09:39
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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

v3.1.3 bugfix of 3.1.2 changes

04 Nov 11:12
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Unfortunately, the changes in the latest release v3.1.2 come with a serious traceback bug that is fixed now.

v3.1.2 - bugfix and region plotting

30 Oct 10:56
8285d48
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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)