Generate DNA Element
Generates random DNA sequences with a given nucleotide content that can be specified manually or evaluated from the reference file.
Element type: generate-dna
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Length | Length of the resulting sequence or sequences. | 1000 bp | length | numeric |
| Count | Number of sequences to generate. | 1 | count | numeric |
| Seed | Value to initialize the random generator. By default (seed = -1), the generator is initialized with the system time. | -1 | seed | numeric |
| Content | Specifies how the nucleotide content of the sequence(s) should be generated. It can be either taken from the reference file or input manually. | manual | content | string |
| Algorithm | Algorithm for generating random sequence(s). Two algorithms are available: GC Content and GC Skew. | GC Content | algorithm | string |
| Window size | The DNA sequence generation is divided into windows of the specified size. In each window, the base ratio is kept. | 1000 | window-size | numeric |
| Reference | Path to the reference file (could be a sequence or an alignment). | reference-url | string | |
| A | Adenine content. | 25% | percent-a | numeric |
| C | Cytosine content. | 25% | percent-c | numeric |
| G | Guanine content. | 25% | percent-g | numeric |
| T | Thymine content. | 25% | percent-t | numeric |
| GC Skew | GC Skew is calculated as (G - C) / (G + C). | 0.25 | gc-skew | numeric |
Available values for Content:
- manual
- reference
Available values for Algorithm:
- gc-content
- gc-skew
Input/Output Ports
The element has 1 output port:
Name in GUI: Sequences
Name in Workflow File: out-sequence
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |