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Up: Component summary
Component
RNAFoldPredicts 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) |
| Issue tracker | View/Report issues |
| 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, |
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