Description

calculate secondary structures of two RNAs with dimerization

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

rnacofold_fasta:file

A fasta file containing RNA or transcript sequences

*.{fasta,fa}

Output

name:type
description
pattern

rnacofold_csv

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.csv:file

The CSV Output of RNAcofold that has the predicted structure and energies

*.{csv}

rnacofold_ps

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.ps:file

The text Output of RNAfold that contains the predicted secondary structure in postscript format

*.{ps}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

viennarna
custom

calculate secondary structures of two RNAs with dimerization The program works much like RNAfold, but allows one to specify two RNA sequences which are then allowed to form a dimer structure. RNA sequences are read from stdin in the usual format, i.e. each line of input corresponds to one sequence, except for lines starting with > which contain the name of the next sequence. To compute the hybrid structure of two molecules, the two sequences must be concatenated using the & character as separator. RNAcofold can compute minimum free energy (mfe) structures, as well as partition function (pf) and base pairing probability matrix (using the -p switch) Since dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers. Output consists of the mfe structure in bracket notation as well as PostScript structure plots and “dot plot” files containing the pair probabilities, see the RNAfold man page for details. In the dot plots a cross marks the chain break between the two concatenated sequences. The program will continue to read new sequences until a line consisting of the single character @ or an end of file condition is encountered.