IntaRNA

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sometimes only the multi-threading libs are installed, which causes linking to the standard libs (without `-mt` suffix) to die.. in that case we might need something like this ``` LIBS="$LIBS...

martin-raden

``` --> IntaRNA -q AACCGUGGCUUUCGAUUGUUAC -t AACCGUGGCUUUCGAUUGUUAC -n 50 --outmode=C --outcsvcols=hybridDPfull,E,ED1,ED2,E_hybrid --outmaxE=-3 --noseed --outnolp # INFO : Since no seed constraint needed: resetting model from 'X' to 'S' hybridDPfull;E;ED1;ED2;E_hybrid ...........((((.......&...........)))).......;-3.7;0;0;-3.7...

martin-raden

Multiple output formats per one run

1

Hi, it is possible to make IntaRNA output two files (two different output setups) like one detailed RNA:RNA interaction file and one customizable CSV file? Or basically any combination of...

trachtok

tackle user feedback: > The only aspect I think confused me was whether sub-optimal matches were talking only about the same position in the UTR/miRNA - with differences in binding...

martin-raden

.. to avoid that fasta files have to be pruned

martin-raden

IntaRNAeval (C++)

1

- create a personality that takes an interaction and provides respective energy and seed assignments

martin-raden

Concentration stuff

2

http://www.nupack.org/partition/info?melt=true&complexes_job=true&page_name=histogram_detail

martin-raden

check literature

1

- global mapping of small RNA interactome: http://www.cell.com/molecular-cell/pdf/S1097-2765(16)30413-0.pdf -ncRNA-mRNA interaction: shuffled controls consistently more stable than real interactions. http://www.slideshare.net/ppgardne/avoidance-of-stochastic-rna-interactions-can-be-harnessed-to-control-protein-expression-levels-in-bacteria-and-archaea - random RR interaction avoidance: https://elifesciences.org/content/5/e20686 https://elifesciences.org/content/5/e13479

martin-raden

one file output output of pairwise spotProb, mfe, etc. information per query or target - q|t defines column indices respectively - other sequence(s) define rows - additional (leading) column with...

martin-raden

Incorporate RNAplex model with seed heuristic

2

- include RNAplex model - enable seed heuristic - enable nested + pseudoknot accessibilities

martin-raden