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| https://anaconda.org/bioconda/intarna |
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| Prof. Backofen's bioinformatics group at Freiburg University | http://www.bioinf.uni-freiburg.de |
| Freiburg RNA tools IntaRNA webserver | http://rna.informatik.uni-freiburg.de/IntaRNA/ |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#contribution |
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| IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions | https://doi.org/10.1093/nar/gkx279 |
| 10.1093/nar/gkx279 | https://doi.org/10.1093/nar/gkx279 |
| IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions | https://doi.org/10.1093/bioinformatics/btn544 |
| 10.1093/bioinformatics/btn544 | https://doi.org/10.1093/bioinformatics/btn544 |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#features-and-application |
| Integration of accessibility data from structure probing into RNA–RNA interaction prediction | https://doi.org/10.1093/bioinformatics/bty1029 |
| 10.1093/bioinformatics/bty1029 | https://doi.org/10.1093/bioinformatics/bty1029 |
| IntaRNAhelix - Composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction | https://doi.org/10.1142/S0219720019400092 |
| 10.1142/S0219720019400092 | https://doi.org/10.1142/S0219720019400092 |
| CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains | https://doi.org/10.1093/nar/gku359 |
| 10.1093/nar/gku359 | https://doi.org/10.1093/nar/gku359 |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#documentation |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| Installation | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#install |
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| Just run ... | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#defaultRun |
| Multi-threading and parallelized computation | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#multithreading |
| Load arguments from file | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#parameterFile |
| General things you should know | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#generalInformation |
| Interaction Model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel |
| Single-site, loop-based RNA-RNA interaction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe |
| Single-site, ensemble-based RNA-RNA interaction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssProbability |
| Single-site, helix-based RNA-RNA interaction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssHelixBlockMfe |
| Prediction modes | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| Emulating other RNA-RNA interaction prediction tools | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predEmulateTools |
| Limiting memory consumption - window-based prediction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predWindowBased |
| IntaRNA's multiple personalities | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#personality |
| IntaRNA - fast, heuristic RNA-RNA interaction prediction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNA |
| IntaRNAhelix - helix-based predictions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAhelix |
| IntaRNAexact - exact predictions like RNAup | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAexact |
| IntaRNAduplex - hybrid-only optimization like RNAduplex | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAduplex |
| IntaRNAsTar - optimized for sRNA-target prediction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAsTar |
| IntaRNAseed - identifys and reports seed interactions only | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAseed |
| IntaRNAens - ensemble-based prediction and partition function computation | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAens |
| How to constrain predicted interactions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#constraintSetup |
| Interaction restrictions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| Seed constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| Explicit seed input | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seedExplicit |
| Helix constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#helix |
| SHAPE reactivity data to enhance accessibility computation | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#shape |
| Output Setup | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#outputSetup |
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| Suboptimal RNA-RNA interaction prediction and output restrictions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
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| Minimal energy for all intermolecular index pairs | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#pairMinE |
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| Accessibility and unpaired probabilities | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility |
| Local versus global unpaired probabilities | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accLocalGlobal |
| Constrain regions to be accessible or blocked | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accConstraints |
| Scaling factors for partition function computation for accessibility estimation | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accPfScale |
| Read/write accessibility from/to file or stream | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accFromFile |
| Library for integration in external tools | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#lib |
| Auxiliary R scripts for output visualization etc. | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/R |
| Auxiliary python scripts for IntaRNA-based pipelines | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/python |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#installation |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarna-via-conda-bioconda-channel |
| bioconda | https://bioconda.github.io/ |
| http://bioconda.github.io/recipes/intarna/README.html |
| Miniconda installation | https://docs.anaconda.com/miniconda/install/#quick-command-line-install |
| consider to first install a Linux App via WSL | https://documentation.ubuntu.com/wsl/en/latest/howto/install-ubuntu-wsl2/ |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarna-docker-container-via-quayio |
| IntaRNA docker container | https://quay.io/repository/biocontainers/intarna |
| ? | https://www.docker.com/ |
| Quay.io | https://quay.io/ |
| quay.io IntaRNA tag page | https://quay.io/repository/biocontainers/intarna?tab=tags |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#dependencies |
| boost C++ library | http://www.boost.org/ |
| Vienna RNA package | http://www.tbi.univie.ac.at/RNA/ |
| cloning from github | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#instgithub |
| Catch | https://github.com/philsquared/Catch |
| Easylogging++ | https://github.com/easylogging/easyloggingpp |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#cloning-source-code-from-github-or-downloading-zip-file |
| IntaRNA release page | https://github.com/BackofenLab/IntaRNA/releases/latest |
| IntaRNA package distribution | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#instsource |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarna-package-distribution-eg-intarna-200targz |
| IntaRNA release page | https://github.com/BackofenLab/IntaRNA/releases/latest |
| dependencies | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#deps |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#microsoft-windows-installation |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#-from-source |
| Cygwin | https://www.cygwin.com/ |
| install from github | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#instgithub |
| install from package | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#instsource |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#-using-pre-compiled-binaries |
| IntaRNA release page | https://github.com/BackofenLab/IntaRNA/releases/latest |
| download | https://github.com/BackofenLab/IntaRNA/releases/latest |
| Windows command prompt | https://www.lifewire.com/how-to-open-command-prompt-2618089 |
| run IntaRNA | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#usage |
| Path System variable | http://www.computerhope.com/issues/ch000549.htm |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#os-x-installation-with-homebrew-thanks-to-lars-barquist |
| bioconda | https://anaconda.org/bioconda/intarna |
| release page | https://github.com/BackofenLab/IntaRNA/releases/latest |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#usage-and-parameters |
| prediction modes | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| interaction models | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel |
| interaction restrictions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| seed constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| explicit seed information | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seedExplicit |
| SHAPE reactivity constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#shape |
| output modes | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#outmodes |
| suboptimal enumeration | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
| energy parameters, temperature | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#energy |
| accessibility | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility |
| multi-threading support | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#multithreading |
| Freiburg RNA tools IntaRNA webserver | http://rna.informatik.uni-freiburg.de/IntaRNA/ |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#just-run- |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#multi-threading-and-parallelized-computation |
| prediction modes | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| window-based prediction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predWindowBased |
| window combinations | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predWindowBased |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#load-arguments-from-file |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#general-things-you-should-know |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#rna-rna-interaction-models |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/interaction-context.svg |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| Interactive implementations of thermodynamics-based RNA structure and RNA-RNA interaction prediction approaches for example-driven teaching. | https://doi.org/10.1371/journal.pcbi.1006341 |
| Structure and interaction prediction in prokaryotic RNA biology. | https://doi.org/10.1128/microbiolspec.RWR-0001-2017 |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#single-site-loop-based-rna-rna-interaction-with-minimal-free-energy |
| IntaRNA | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNA |
| IntaRNAexact | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAexact |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#single-site-ensemble-based-rna-rna-interaction-with-minimal-free-ensemble-energy |
| CSV output | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#outModeCsv |
| CSV output | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#outModeCsv |
| IntaRNAens | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAens |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#helix-based-single-site-rna-rna-interaction-with-minimal-free-energy |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/helixbased.svg |
| helix constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#helix |
| IntaRNAhelix | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAhelix |
| IntaRNAhelix - Composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction | https://doi.org/10.1142/S0219720019400092 |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#prediction-modes |
| Seed constraint | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| Explicit seeds | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seedExplicit |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| SHAPE reactivity constraint | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#shape |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| seed constraint | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-no.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| suboptimal interactions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| suboptimal interactions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-no.39.png |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#emulating-other-rna-rna-interaction-prediction-tools |
| IntaRNAexact personality | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAexact |
| IntaRNAexact personality | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#IntaRNAexact |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#limiting-memory-consumption---window-based-prediction |
| --q|tIntLenMax | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| parallelized | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#multithreading |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnas-multiple-personalities |
| interaction models | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel |
| prediction modi | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarna |
| (Busch et al., 2008) | https://doi.org/10.1093/bioinformatics/btn544 |
| (Mann et al., 2017) | https://doi.org/10.1093/nar/gkx279 |
| prediction mode | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| accessibility | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accLocalGlobal |
| interaction models | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarna1-and-intarna2 |
| prediction strategy | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe |
| energy set | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#energy |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnaexact |
| interaction models | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe |
| prediction modes | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| RNAup-like predictions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predEmulateTools |
| prediction mode | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| interaction length | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| accessibility | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accLocalGlobal |
| overlap in both RNAs | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
| seed constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| seed-extension-based computation model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModel |
| regions of
interest | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| constraint the seed regions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnahelix |
| (Gelhausen et al., 2019) | https://doi.org/10.1142/S0219720019400092 |
| helix-based single-site interaction model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssHelixBlockMfe |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnaduplex |
| accessibility | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility |
| heuristic prediction mode | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| seed constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnastar |
| no GU base pairs in seeds | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| minimal unpaired probability of 0.001 of seed regions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed |
| maximal interaction length of 60 | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| maximal interior loop size of 8 | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#energy |
| minimal unpaired probability of 0.001 of interacting regions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| no GU base pairs at helix or interaction ends | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| no lonely base pairs | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interConstr |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnaseed |
| seed-only prediction mode | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#intarnaens |
| ensemble-based predictions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssProbability |
| ensemble-based prediction model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssProbability |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#how-to-constrain-predicted-interactions |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interaction-restrictions |
| suboptimal interaction prediction | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seed-constraints |
| explicit seed interactions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#seedExplicit |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#explicit-seed-input |
| below | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#outModeCsv |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#helix-constraints |
| helix-based interaction models | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel-ssHelixBlockMfe |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#shape-reactivity-data-to-enhance-accessibility-computation |
| 2015 | https://doi.org/10.1093/bioinformatics/btv523 |
| 2016 | https://dx.doi.org/10.1186%2Fs13015-016-0070-z |
| RNAfold manpage | https://www.tbi.univie.ac.at/RNA/RNAfold.1.html |
| RNAfold manpage | https://www.tbi.univie.ac.at/RNA/RNAfold.1.html |
| Integration of accessibility data from structure probing into RNA-RNA interaction prediction. | https://doi.org/10.1093/bioinformatics/bty1029 |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#output-setup |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#output-modes |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#standard-rna-rna-interaction-output-with-ascii-chart |
| Just run ... | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#defaultRun |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#detailed-rna-rna-interaction-output-with-ascii-chart |
| accessibility | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#customizable-csv-rna-rna-interaction-output |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#ensemble-output-of-considered-rna-rna-interactions |
| prediction mode | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#predModes |
| RNA-RNA interaction model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interactionModel |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#pairwise-vs-all-vs-all |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#sequence-indexing |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#suboptimal-rna-rna-interaction-prediction-and-output-restrictions |
| blocked | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accConstraints |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#energy-parameters-and-temperatures |
| accessibility constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accConstraints |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#additional-output-files |
| query/target's spot probability profile | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#profileSpotProb |
| all spot probabilities | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#spotProb |
| the query/target's minimal interaction energy profile | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/profileMinE |
| minimal interaction energy for all query-target index pairs | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/pairMinE |
| query/target's ED accessibility values | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility |
| query/target's unpaired probabilities | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#minimal-energy-profiles |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#minimal-energy-for-all-intermolecular-index-pairs |
| minimal energy profile | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#profileMinE |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/blob/master/doc/figures/pair-minE.png |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#spot-probability-profiles |
| minimal energy profiles | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#profileMinE |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#interaction-probabilities-for-interaction-spots-of-interest |
| SHAPE data | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#shape |
| structure/accessibility constraints | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accConstraints |
| discussion about suboptimal interactions | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#subopts |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#spot-probabilities-for-all-intermolecular-index-pairs |
| minimal energy heatmap | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#pairMinE |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#accessibility-and-unpaired-probabilities |
| energy model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#energy |
| energy model | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#energy |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#local-versus-global-unpaired-probabilities |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#use-case-examples-globallocal-unpaired-probability-computation |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#constraints-for-accessibility-computation |
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| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#scaling-factors-for-partition-function-computation-for-accessibility-estimation |
| RNAplfold manual | https://www.tbi.univie.ac.at/RNA/RNAplfold.1.html |
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| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#readwrite-accessibility-fromto-file-or-stream |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#use-case-examples-for-readwrite-accessibilities-and-unpaired-probabilities |
| back to overview | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#overview |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#library-for-integration-in-external-tools |
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA#mandatory-easylogging-initalization- |
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| backofenlab.github.io/IntaRNA/ | https://backofenlab.github.io/IntaRNA/ |
|
bioinformatics
| https://patch-diff.githubusercontent.com/topics/bioinformatics |
|
tool
| https://patch-diff.githubusercontent.com/topics/tool |
|
structure
| https://patch-diff.githubusercontent.com/topics/structure |
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rna
| https://patch-diff.githubusercontent.com/topics/rna |
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interaction
| https://patch-diff.githubusercontent.com/topics/interaction |
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Readme
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Unknown
LICENSE
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Activity | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/activity |
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Custom properties | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/custom-properties |
|
49
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8
watching | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/watchers |
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28
forks | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/forks |
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Report repository
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| Releases
30 | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/releases |
|
3.4.1 - bugfix explizit seeds and seed order check
Latest
Sep 18, 2024
| https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/releases/tag/v3.4.1 |
| + 29 releases | https://patch-diff.githubusercontent.com/BackofenLab/IntaRNA/releases |
| Packages
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|
C++
90.9%
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M4
4.6%
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Python
2.9%
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Makefile
0.5%
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R
0.5%
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Perl
0.4%
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