3.3.2 - bugfix IntaRNAhelix

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

IntaRNA

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

3.3.0 - pairwise sequence processing

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

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

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

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

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`

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

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

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)