Martin Raden

Hi @sjanssen2 many thanks for your feedback. All arrows in the matrices represent **optimal** tracebacks, ie. not computation ways but traces that produce the value within the clicked cell. Thus,...

Hi Christian, did you activate the environment before calling "IntaRNA --version" ? Try ``` conda activate IntaRNA IntaRNA --version ``` You can [check the active conda environment](https://stackoverflow.com/questions/58369272/check-what-conda-environment-is-currently-activated) using `conda info`...

PS. most likely your conda base installation features an old IntaRNA version or an old IntaRNA is installed in your system in one of the default PATHs and thus called...

Hi Christian, sorry for the late reply. You are right, eventually conda should deal with that and set pathes accordingly with higher priority to your environment installation. Maybe your conda...

Nupack user guide

coming soon...

Hi @paolabc, thanks for your question and detailed check. Eventually, given your command line arguments, I guess **you are using the outdated original IntaRNA version 1 !!!!** You get the...

## accessibility computation models to be tested - RNAplex - Accessfold - NUPACK-based

## concerning NUPACK NUPACK enables the computation of (position-wise) unpaired probabilities. These could be incorporated in a AccessFold-like approach to incorporate pseudoknotted intramolecular structure into the interaction prediction. Two options:...

related: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-1-r16 CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data