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RNAFold

Predicts RNA secondary structure using Vienna RNA Package energy minimization function.

Version 1.0
Bundle microarray
Categories Sequence Motif Annotation
Authors Erkka Valo (erkka.valo@helsinki.fi)
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Requires RNAsubopt (Vienna RNA package) ; installer (bash)
Source files component.xml RNAFold.java
Usage Example with default values

Inputs

Name Type Mandatory Description
sequence CSV Mandatory A CSV file containing sequences in one of the columns

Outputs

Name Type Description
structure CSV A CSV file containing the predicted secondary structures and it's free energy.

Parameters

Name Type Default Description
e float 1 Calculate suboptimal structures within the e kcal/mol of the mfe.
idColumn string "" Name of the column containing the ids for the sequences.
noLP boolean false Only produce structures without lonely pairs (helices of length 1). This reduces the number of structures drastically and should therefore be used for longer sequences and larger energy ranges.
program string "RNAsubopt" The program used to predict the RNA secondary structure. Only RNAsubopt is supported.
seqColumn string "" Name of the column containing the sequences.
temp float 37 Temperature at which the prediction is done.

Test cases

Test case Parameters IN
sequence
OUT
structure
case1 properties sequence structure

seqColumn=rna_sequence,
idColumn=id,
program=RNAsubopt,
e=1,
noLP=true


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