Generates random DNA sequences with 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 resulted 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 (see the Referenceparameter), or input manually. | manual | content | string |
| Algorithm | Algorithm for generating random sequence(s). Two algorithms are available: GC Content and GC Skew. If you choose GC Content, then parameters A,C, G, T are used to generate the sequence. Otherwise, the GC Skewparameter is used to generate the sequence(s). | GC Content | algorithm | string Available values are:
|
| Window size | The DNA sequence generation is divided into windows of the specified size. In each window the bases ratio, defined by other parameters, is kept. | 1000 | window-size | numeric |
| Reference | Path to the reference file (could be a sequence or an alignment). | reference-url | string Available values are:
| |
| 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), where G is the number of G’s in the window, and C is the number of C’s. | 0.25 | gc-skew | numeric |
Input/Output Ports
The element has 1 output port:
Name in GUI: Sequences
Name in Workflow File: out-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |