Releases: BackofenLab/IntaRNA
Releases · BackofenLab/IntaRNA
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 namingacc|accW|accL
: meta accessibility setup for both query and targetintLenMax|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
andseed?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 valuesIntaRNA_plotRegions.R
= renaming of formerplotRegions.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
- new ensemble energy and partition function output for intra-molecular
- 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)