IntaRNA

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[helix-based] context-sensitive helix-based predictions

1

given the [helix-based RNA-RNA interaction prediction mode](http://www.bioinf.uni-freiburg.de/Publications/Gelhausen-helixLength-2019.pdf), we want to apply context-sensitive length constraints. needed: - HelixHandler wrapper for length-constrained helices - AccessibilityVRNA subclass that stores context-dependent ED values -...

martin-raden

[helix-based] ideas for improvements

1

- enforce GC ends (ala pkKnots) - no GU end - minimal E of terminal loops might be useful for seed filtering as well ... - check how to combine...

martin-raden

+ add CSV output mode

martin-raden

see [RNAfold manpage](https://www.tbi.univie.ac.at/RNA/RNAfold.1.html)

martin-raden

python wrapper via pybind11 or boost::python

1

https://www.boost.org/doc/libs/1_64_0/libs/python/doc/html/index.html

martin-raden

[helix-based] optimize bulge breakpoint

5

I found an example where a shift of a one-sided bulge causes a significant energy change (in `--mode=H`) ``` --> IntaRNA -q GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUUUUU -t CUGGAUGAAUGACAGGGAAAACAUGCGUAAUACUUACGCAGUUCUCUGAAAAAGUGAUUUAAAUUUAGAUGGAUAGCGGUGUAUGGAAACGUUCUGUUACAUGAAAUGGCCCGUUAGACAUCACAAAUCGCGAAGAGUUUCCCAUUAAUUUUUGAUAUAUUUAAAACUUAGGACUUAUUUGAAUCACAUUUGAGGUGGUUAUGAAAAAAAUUGCAUGUCUUUCAGCACUGGCCGCAGUUCUGGCUUUCACCGCAGGUACUUCCGUAGCUGCGACUUCUACUGUAACUGGCGGUUACGCAC --mode=H ``` ### default mode...

martin-raden

Allow Multi loops in interaction region

8

PatrickRWright

- `parse_region_from_genome.pl` - ... check what can be transfered from IntaRNA_wrapper

martin-raden

IntaRNAsTar Exception raised

2

Hi, I am running IntaRNAsTar with a genome and list of sRNAs both in fasta format. I ran the following on the command line: IntaRNAsTar -t target.file -q query.file --out...

meichelman

martin-raden