René's URL Explorer Experiment


Title: GitHub - BackofenLab/IntaRNA: Efficient target prediction incorporating accessibility of interaction sites · GitHub

Open Graph Title: GitHub - BackofenLab/IntaRNA: Efficient target prediction incorporating accessibility of interaction sites

X Title: GitHub - BackofenLab/IntaRNA: Efficient target prediction incorporating accessibility of interaction sites

Description: Efficient target prediction incorporating accessibility of interaction sites - BackofenLab/IntaRNA

Open Graph Description: Efficient target prediction incorporating accessibility of interaction sites - BackofenLab/IntaRNA

X Description: Efficient target prediction incorporating accessibility of interaction sites - BackofenLab/IntaRNA

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autotools-init.shhttps://github.com/BackofenLab/IntaRNA/blob/master/autotools-init.sh
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conda-build-env.ymlhttps://github.com/BackofenLab/IntaRNA/blob/master/conda-build-env.yml
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https://github.com/BackofenLab/IntaRNA/releases
https://anaconda.org/bioconda/intarna
https://github.com/BackofenLab/IntaRNA#intarna---
Prof. Backofen's bioinformatics group at Freiburg Universityhttp://www.bioinf.uni-freiburg.de
Freiburg RNA tools IntaRNA webserverhttp://rna.informatik.uni-freiburg.de/IntaRNA/
https://github.com/BackofenLab/IntaRNA#contribution
Issueshttps://github.com/BackofenLab/IntaRNA/issues
https://github.com/BackofenLab/IntaRNA#citation
https://github.com/BackofenLab/IntaRNA#method
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactionshttps://doi.org/10.1093/nar/gkx279
10.1093/nar/gkx279https://doi.org/10.1093/nar/gkx279
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regionshttps://doi.org/10.1093/bioinformatics/btn544
10.1093/bioinformatics/btn544https://doi.org/10.1093/bioinformatics/btn544
https://github.com/BackofenLab/IntaRNA#features-and-application
Integration of accessibility data from structure probing into RNA–RNA interaction predictionhttps://doi.org/10.1093/bioinformatics/bty1029
10.1093/bioinformatics/bty1029https://doi.org/10.1093/bioinformatics/bty1029
IntaRNAhelix - Composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target predictionhttps://doi.org/10.1142/S0219720019400092
10.1142/S0219720019400092https://doi.org/10.1142/S0219720019400092
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domainshttps://doi.org/10.1093/nar/gku359
10.1093/nar/gku359https://doi.org/10.1093/nar/gku359
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessmenthttps://doi.org/10.1186/s12859-019-3143-4
10.1186/s12859-019-3143-4https://doi.org/10.1186/s12859-019-3143-4
https://github.com/BackofenLab/IntaRNA#documentation
https://github.com/BackofenLab/IntaRNA#overview
Installationhttps://github.com/BackofenLab/IntaRNA#install
IntaRNA via condahttps://github.com/BackofenLab/IntaRNA#instconda
IntaRNA docker containerhttps://github.com/BackofenLab/IntaRNA#instdocker
Dependencieshttps://github.com/BackofenLab/IntaRNA#deps
Cloning from githubhttps://github.com/BackofenLab/IntaRNA#instgithub
Source code distributionhttps://github.com/BackofenLab/IntaRNA#instsource
Microsoft Windows installationhttps://github.com/BackofenLab/IntaRNA#instwin
OS X installation with homebrewhttps://github.com/BackofenLab/IntaRNA#instosx
Usage and Parametershttps://github.com/BackofenLab/IntaRNA#usage
Just run ...https://github.com/BackofenLab/IntaRNA#defaultRun
Multi-threading and parallelized computationhttps://github.com/BackofenLab/IntaRNA#multithreading
Load arguments from filehttps://github.com/BackofenLab/IntaRNA#parameterFile
General things you should knowhttps://github.com/BackofenLab/IntaRNA#generalInformation
Interaction Modelhttps://github.com/BackofenLab/IntaRNA#interactionModel
Single-site, loop-based RNA-RNA interactionhttps://github.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe
Single-site, ensemble-based RNA-RNA interactionhttps://github.com/BackofenLab/IntaRNA#interactionModel-ssProbability
Single-site, helix-based RNA-RNA interactionhttps://github.com/BackofenLab/IntaRNA#interactionModel-ssHelixBlockMfe
Prediction modeshttps://github.com/BackofenLab/IntaRNA#predModes
Emulating other RNA-RNA interaction prediction toolshttps://github.com/BackofenLab/IntaRNA#predEmulateTools
Limiting memory consumption - window-based predictionhttps://github.com/BackofenLab/IntaRNA#predWindowBased
IntaRNA's multiple personalitieshttps://github.com/BackofenLab/IntaRNA#personality
IntaRNA - fast, heuristic RNA-RNA interaction predictionhttps://github.com/BackofenLab/IntaRNA#IntaRNA
IntaRNAhelix - helix-based predictionshttps://github.com/BackofenLab/IntaRNA#IntaRNAhelix
IntaRNAexact - exact predictions like RNAuphttps://github.com/BackofenLab/IntaRNA#IntaRNAexact
IntaRNAduplex - hybrid-only optimization like RNAduplexhttps://github.com/BackofenLab/IntaRNA#IntaRNAduplex
IntaRNAsTar - optimized for sRNA-target predictionhttps://github.com/BackofenLab/IntaRNA#IntaRNAsTar
IntaRNAseed - identifys and reports seed interactions onlyhttps://github.com/BackofenLab/IntaRNA#IntaRNAseed
IntaRNAens - ensemble-based prediction and partition function computationhttps://github.com/BackofenLab/IntaRNA#IntaRNAens
How to constrain predicted interactionshttps://github.com/BackofenLab/IntaRNA#constraintSetup
Interaction restrictionshttps://github.com/BackofenLab/IntaRNA#interConstr
Seed constraintshttps://github.com/BackofenLab/IntaRNA#seed
Explicit seed inputhttps://github.com/BackofenLab/IntaRNA#seedExplicit
Helix constraintshttps://github.com/BackofenLab/IntaRNA#helix
SHAPE reactivity data to enhance accessibility computationhttps://github.com/BackofenLab/IntaRNA#shape
Output Setuphttps://github.com/BackofenLab/IntaRNA#outputSetup
Output modeshttps://github.com/BackofenLab/IntaRNA#outmodes
Pairwise vs. all-vs-allhttps://github.com/BackofenLab/IntaRNA#outpairwise
Sequence indexinghttps://github.com/BackofenLab/IntaRNA#idxPos0
Suboptimal RNA-RNA interaction prediction and output restrictionshttps://github.com/BackofenLab/IntaRNA#subopts
Energy parameters and temperaturehttps://github.com/BackofenLab/IntaRNA#energy
Additional output fileshttps://github.com/BackofenLab/IntaRNA#outFiles
Minimal energy profileshttps://github.com/BackofenLab/IntaRNA#profileMinE
Minimal energy for all intermolecular index pairshttps://github.com/BackofenLab/IntaRNA#pairMinE
Spot probability profileshttps://github.com/BackofenLab/IntaRNA#profileSpotProb
Interaction probabilities for interaction spots of interesthttps://github.com/BackofenLab/IntaRNA#spotProb
Accessibility and unpaired probabilitieshttps://github.com/BackofenLab/IntaRNA#accessibility
Local versus global unpaired probabilitieshttps://github.com/BackofenLab/IntaRNA#accLocalGlobal
Constrain regions to be accessible or blockedhttps://github.com/BackofenLab/IntaRNA#accConstraints
Scaling factors for partition function computation for accessibility estimationhttps://github.com/BackofenLab/IntaRNA#accPfScale
Read/write accessibility from/to file or streamhttps://github.com/BackofenLab/IntaRNA#accFromFile
Library for integration in external toolshttps://github.com/BackofenLab/IntaRNA#lib
Auxiliary R scripts for output visualization etc.https://github.com/BackofenLab/IntaRNA/blob/master/R
Auxiliary python scripts for IntaRNA-based pipelineshttps://github.com/BackofenLab/IntaRNA/blob/master/python
https://github.com/BackofenLab/IntaRNA#installation
https://github.com/BackofenLab/IntaRNA#intarna-via-conda-bioconda-channel
biocondahttps://bioconda.github.io/
http://bioconda.github.io/recipes/intarna/README.html
Miniconda installationhttps://docs.anaconda.com/miniconda/install/#quick-command-line-install
consider to first install a Linux App via WSLhttps://documentation.ubuntu.com/wsl/en/latest/howto/install-ubuntu-wsl2/
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarna-docker-container-via-quayio
IntaRNA docker containerhttps://quay.io/repository/biocontainers/intarna
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quay.io IntaRNA tag pagehttps://quay.io/repository/biocontainers/intarna?tab=tags
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https://github.com/BackofenLab/IntaRNA#dependencies
boost C++ libraryhttp://www.boost.org/
Vienna RNA packagehttp://www.tbi.univie.ac.at/RNA/
cloning from githubhttps://github.com/BackofenLab/IntaRNA#instgithub
Catchhttps://github.com/philsquared/Catch
Easylogging++https://github.com/easylogging/easyloggingpp
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#cloning-source-code-from-github-or-downloading-zip-file
IntaRNA release pagehttps://github.com/BackofenLab/IntaRNA/releases/latest
IntaRNA package distributionhttps://github.com/BackofenLab/IntaRNA#instsource
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarna-package-distribution-eg-intarna-200targz
IntaRNA release pagehttps://github.com/BackofenLab/IntaRNA/releases/latest
dependencieshttps://github.com/BackofenLab/IntaRNA#deps
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#microsoft-windows-installation
https://github.com/BackofenLab/IntaRNA#-from-source
Cygwinhttps://www.cygwin.com/
install from githubhttps://github.com/BackofenLab/IntaRNA#instgithub
install from packagehttps://github.com/BackofenLab/IntaRNA#instsource
https://github.com/BackofenLab/IntaRNA#-using-pre-compiled-binaries
IntaRNA release pagehttps://github.com/BackofenLab/IntaRNA/releases/latest
downloadhttps://github.com/BackofenLab/IntaRNA/releases/latest
Windows command prompthttps://www.lifewire.com/how-to-open-command-prompt-2618089
run IntaRNAhttps://github.com/BackofenLab/IntaRNA#usage
Path System variablehttp://www.computerhope.com/issues/ch000549.htm
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#os-x-installation-with-homebrew-thanks-to-lars-barquist
biocondahttps://anaconda.org/bioconda/intarna
release pagehttps://github.com/BackofenLab/IntaRNA/releases/latest
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#usage-and-parameters
prediction modeshttps://github.com/BackofenLab/IntaRNA#predModes
interaction modelshttps://github.com/BackofenLab/IntaRNA#interactionModel
interaction restrictionshttps://github.com/BackofenLab/IntaRNA#interConstr
seed constraintshttps://github.com/BackofenLab/IntaRNA#seed
explicit seed informationhttps://github.com/BackofenLab/IntaRNA#seedExplicit
SHAPE reactivity constraintshttps://github.com/BackofenLab/IntaRNA#shape
output modeshttps://github.com/BackofenLab/IntaRNA#outmodes
suboptimal enumerationhttps://github.com/BackofenLab/IntaRNA#subopts
energy parameters, temperaturehttps://github.com/BackofenLab/IntaRNA#energy
accessibilityhttps://github.com/BackofenLab/IntaRNA#accessibility
multi-threading supporthttps://github.com/BackofenLab/IntaRNA#multithreading
Freiburg RNA tools IntaRNA webserverhttp://rna.informatik.uni-freiburg.de/IntaRNA/
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#just-run-
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#multi-threading-and-parallelized-computation
prediction modeshttps://github.com/BackofenLab/IntaRNA#predModes
window-based predictionhttps://github.com/BackofenLab/IntaRNA#predWindowBased
window combinationshttps://github.com/BackofenLab/IntaRNA#predWindowBased
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#load-arguments-from-file
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#general-things-you-should-know
https://github.com/BackofenLab/IntaRNA#rna-rna-interaction-models
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/interaction-context.svg
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.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 overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#single-site-loop-based-rna-rna-interaction-with-minimal-free-energy
IntaRNAhttps://github.com/BackofenLab/IntaRNA#IntaRNA
IntaRNAexacthttps://github.com/BackofenLab/IntaRNA#IntaRNAexact
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#single-site-ensemble-based-rna-rna-interaction-with-minimal-free-ensemble-energy
CSV outputhttps://github.com/BackofenLab/IntaRNA#outModeCsv
CSV outputhttps://github.com/BackofenLab/IntaRNA#outModeCsv
IntaRNAenshttps://github.com/BackofenLab/IntaRNA#IntaRNAens
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#helix-based-single-site-rna-rna-interaction-with-minimal-free-energy
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/helixbased.svg
helix constraintshttps://github.com/BackofenLab/IntaRNA#helix
IntaRNAhelixhttps://github.com/BackofenLab/IntaRNA#IntaRNAhelix
IntaRNAhelix - Composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target predictionhttps://doi.org/10.1142/S0219720019400092
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#prediction-modes
Seed constrainthttps://github.com/BackofenLab/IntaRNA#seed
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
Explicit seedshttps://github.com/BackofenLab/IntaRNA#seedExplicit
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
SHAPE reactivity constrainthttps://github.com/BackofenLab/IntaRNA#shape
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
seed constrainthttps://github.com/BackofenLab/IntaRNA#seed
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-no.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
suboptimal interactionshttps://github.com/BackofenLab/IntaRNA#subopts
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
suboptimal interactionshttps://github.com/BackofenLab/IntaRNA#subopts
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-no.39.png
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/icon-yes.39.png
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#emulating-other-rna-rna-interaction-prediction-tools
IntaRNAexact personalityhttps://github.com/BackofenLab/IntaRNA#IntaRNAexact
IntaRNAexact personalityhttps://github.com/BackofenLab/IntaRNA#IntaRNAexact
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#limiting-memory-consumption---window-based-prediction
--q|tIntLenMaxhttps://github.com/BackofenLab/IntaRNA#interConstr
parallelizedhttps://github.com/BackofenLab/IntaRNA#multithreading
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnas-multiple-personalities
interaction modelshttps://github.com/BackofenLab/IntaRNA#interactionModel
prediction modihttps://github.com/BackofenLab/IntaRNA#predModes
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.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 modehttps://github.com/BackofenLab/IntaRNA#predModes
accessibilityhttps://github.com/BackofenLab/IntaRNA#accLocalGlobal
interaction modelshttps://github.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe
https://github.com/BackofenLab/IntaRNA#intarna1-and-intarna2
prediction strategyhttps://github.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe
energy sethttps://github.com/BackofenLab/IntaRNA#energy
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnaexact
interaction modelshttps://github.com/BackofenLab/IntaRNA#interactionModel-ssUnconstraintMfe
prediction modeshttps://github.com/BackofenLab/IntaRNA#predModes
RNAup-like predictionshttps://github.com/BackofenLab/IntaRNA#predEmulateTools
prediction modehttps://github.com/BackofenLab/IntaRNA#predModes
interaction lengthhttps://github.com/BackofenLab/IntaRNA#interConstr
accessibilityhttps://github.com/BackofenLab/IntaRNA#accLocalGlobal
overlap in both RNAshttps://github.com/BackofenLab/IntaRNA#subopts
seed constraintshttps://github.com/BackofenLab/IntaRNA#seed
seed-extension-based computation modelhttps://github.com/BackofenLab/IntaRNA#predModel
regions of interesthttps://github.com/BackofenLab/IntaRNA#interConstr
constraint the seed regionshttps://github.com/BackofenLab/IntaRNA#seed
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnahelix
(Gelhausen et al., 2019)https://doi.org/10.1142/S0219720019400092
helix-based single-site interaction modelhttps://github.com/BackofenLab/IntaRNA#interactionModel-ssHelixBlockMfe
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnaduplex
accessibilityhttps://github.com/BackofenLab/IntaRNA#accessibility
heuristic prediction modehttps://github.com/BackofenLab/IntaRNA#predModes
seed constraintshttps://github.com/BackofenLab/IntaRNA#seed
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnastar
(Raden et al., 2020)https://doi.org/10.1186/s12859-019-3143-4
no GU base pairs in seedshttps://github.com/BackofenLab/IntaRNA#seed
minimal unpaired probability of 0.001 of seed regionshttps://github.com/BackofenLab/IntaRNA#seed
maximal interaction length of 60https://github.com/BackofenLab/IntaRNA#interConstr
maximal interior loop size of 8https://github.com/BackofenLab/IntaRNA#energy
minimal unpaired probability of 0.001 of interacting regionshttps://github.com/BackofenLab/IntaRNA#interConstr
no GU base pairs at helix or interaction endshttps://github.com/BackofenLab/IntaRNA#interConstr
no lonely base pairshttps://github.com/BackofenLab/IntaRNA#interConstr
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnaseed
seed-only prediction modehttps://github.com/BackofenLab/IntaRNA#predModes
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#intarnaens
ensemble-based predictionshttps://github.com/BackofenLab/IntaRNA#interactionModel-ssProbability
ensemble-based prediction modelhttps://github.com/BackofenLab/IntaRNA#interactionModel-ssProbability
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#how-to-constrain-predicted-interactions
https://github.com/BackofenLab/IntaRNA#interaction-restrictions
suboptimal interaction predictionhttps://github.com/BackofenLab/IntaRNA#subopts
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#seed-constraints
explicit seed interactionshttps://github.com/BackofenLab/IntaRNA#seedExplicit
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#explicit-seed-input
belowhttps://github.com/BackofenLab/IntaRNA#outModeCsv
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#helix-constraints
helix-based interaction modelshttps://github.com/BackofenLab/IntaRNA#interactionModel-ssHelixBlockMfe
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#shape-reactivity-data-to-enhance-accessibility-computation
2015https://doi.org/10.1093/bioinformatics/btv523
2016https://dx.doi.org/10.1186%2Fs13015-016-0070-z
RNAfold manpagehttps://www.tbi.univie.ac.at/RNA/RNAfold.1.html
RNAfold manpagehttps://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 overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#output-setup
https://github.com/BackofenLab/IntaRNA#output-modes
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#standard-rna-rna-interaction-output-with-ascii-chart
Just run ...https://github.com/BackofenLab/IntaRNA#defaultRun
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#detailed-rna-rna-interaction-output-with-ascii-chart
accessibilityhttps://github.com/BackofenLab/IntaRNA#accessibility
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#customizable-csv-rna-rna-interaction-output
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#ensemble-output-of-considered-rna-rna-interactions
prediction modehttps://github.com/BackofenLab/IntaRNA#predModes
RNA-RNA interaction modelhttps://github.com/BackofenLab/IntaRNA#interactionModel
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#pairwise-vs-all-vs-all
https://github.com/BackofenLab/IntaRNA#sequence-indexing
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#suboptimal-rna-rna-interaction-prediction-and-output-restrictions
blockedhttps://github.com/BackofenLab/IntaRNA#accConstraints
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#energy-parameters-and-temperatures
accessibility constraintshttps://github.com/BackofenLab/IntaRNA#accConstraints
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#additional-output-files
query/target's spot probability profilehttps://github.com/BackofenLab/IntaRNA#profileSpotProb
all spot probabilitieshttps://github.com/BackofenLab/IntaRNA#spotProb
the query/target's minimal interaction energy profilehttps://github.com/BackofenLab/IntaRNA/blob/master/profileMinE
minimal interaction energy for all query-target index pairshttps://github.com/BackofenLab/IntaRNA/blob/master/pairMinE
query/target's ED accessibility valueshttps://github.com/BackofenLab/IntaRNA#accessibility
query/target's unpaired probabilitieshttps://github.com/BackofenLab/IntaRNA#accessibility
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#minimal-energy-profiles
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#minimal-energy-for-all-intermolecular-index-pairs
minimal energy profilehttps://github.com/BackofenLab/IntaRNA#profileMinE
https://github.com/BackofenLab/IntaRNA/blob/master/doc/figures/pair-minE.png
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#spot-probability-profiles
minimal energy profileshttps://github.com/BackofenLab/IntaRNA#profileMinE
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#interaction-probabilities-for-interaction-spots-of-interest
SHAPE datahttps://github.com/BackofenLab/IntaRNA#shape
structure/accessibility constraintshttps://github.com/BackofenLab/IntaRNA#accConstraints
discussion about suboptimal interactionshttps://github.com/BackofenLab/IntaRNA#subopts
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#spot-probabilities-for-all-intermolecular-index-pairs
minimal energy heatmaphttps://github.com/BackofenLab/IntaRNA#pairMinE
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#accessibility-and-unpaired-probabilities
energy modelhttps://github.com/BackofenLab/IntaRNA#energy
energy modelhttps://github.com/BackofenLab/IntaRNA#energy
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#local-versus-global-unpaired-probabilities
https://github.com/BackofenLab/IntaRNA#use-case-examples-globallocal-unpaired-probability-computation
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#constraints-for-accessibility-computation
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#scaling-factors-for-partition-function-computation-for-accessibility-estimation
RNAplfold manualhttps://www.tbi.univie.ac.at/RNA/RNAplfold.1.html
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#readwrite-accessibility-fromto-file-or-stream
https://github.com/BackofenLab/IntaRNA#use-case-examples-for-readwrite-accessibilities-and-unpaired-probabilities
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#library-for-integration-in-external-tools
https://github.com/BackofenLab/IntaRNA#mandatory-easylogging-initalization-
back to overviewhttps://github.com/BackofenLab/IntaRNA#overview
https://github.com/BackofenLab/IntaRNA#attributions
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https://www.freepik.com/free-vector/colored-arrows_794372.htm
backofenlab.github.io/IntaRNA/https://backofenlab.github.io/IntaRNA/
bioinformatics https://github.com/topics/bioinformatics
tool https://github.com/topics/tool
structure https://github.com/topics/structure
rna https://github.com/topics/rna
interaction https://github.com/topics/interaction
Readme https://github.com/BackofenLab/IntaRNA#readme-ov-file
Unknown LICENSE https://github.com/BackofenLab/IntaRNA/blob/master/LICENSE
Unknown COPYING https://github.com/BackofenLab/IntaRNA/blob/master/COPYING
Please reload this pagehttps://github.com/BackofenLab/IntaRNA
Activityhttps://github.com/BackofenLab/IntaRNA/activity
Custom propertieshttps://github.com/BackofenLab/IntaRNA/custom-properties
28 forkshttps://github.com/BackofenLab/IntaRNA/forks
Report repository https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FBackofenLab%2FIntaRNA&report=BackofenLab+%28user%29
Releases 30https://github.com/BackofenLab/IntaRNA/releases
3.4.1 - bugfix explizit seeds and seed order check Latest Sep 18, 2024 https://github.com/BackofenLab/IntaRNA/releases/tag/v3.4.1
+ 29 releaseshttps://github.com/BackofenLab/IntaRNA/releases
Packages 0https://github.com/orgs/BackofenLab/packages?repo_name=IntaRNA
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Contributorshttps://github.com/BackofenLab/IntaRNA/graphs/contributors
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C++ 90.9% https://github.com/BackofenLab/IntaRNA/search?l=c%2B%2B
M4 4.6% https://github.com/BackofenLab/IntaRNA/search?l=m4
Python 2.9% https://github.com/BackofenLab/IntaRNA/search?l=python
Makefile 0.5% https://github.com/BackofenLab/IntaRNA/search?l=makefile
R 0.5% https://github.com/BackofenLab/IntaRNA/search?l=r
Perl 0.4% https://github.com/BackofenLab/IntaRNA/search?l=perl
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