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
Assets
4
IntaRNA
- bugfix generation and tracing of seeds with bulges and no GU ends (combination of
seedNoGUendandseed?MaxUP> 0) - bugfix seed-extension prediction for seeds with bulges (
seed?MaxUP> 0) outNoLPfor seeds with bulges enabled (seed?MaxUP> 0)
auxiliary R scripts
IntaRNA_CSV_p-value.Rscript to estimate p-values based on energy valuesIntaRNA_plotRegions.R= renaming of formerplotRegions.R
Assets
4
IntaRNA :
- bugfix traceback of interactions with seed on right-boundary
- bugfix traceback of seeds with bulges when outNoLP present
Assets
4
Unfortunately, the changes in the latest release v3.1.2 come with a serious traceback bug that is fixed now.
Assets
4
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
RToutput - new
bpListoutput
- new ensemble energy and partition function output for intra-molecular
- ensemble output:
Eall1|2EallTotalRT
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):
Assets
3
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):
Assets
3
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.
Assets
4
New Features:
IntaRNA
- overall partitition function estimates
Zalland 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)
intarnapvaluepython3 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 (wasQ) --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--outNoLPsupport 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):
Assets
4
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_Ethat are (for all considered interactions) the overall ensemble energy, overall partition function and the interaction probability for the current interaction (i.e. line)
- enables the CSV output columns
- new
--mode=Sfor 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
--tIntLoopLenand--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.