Generates random DNA sequences with given nucleotide content that can be specified manually or evaluated from the reference file.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Length | Length of the resulted sequence or sequences. | 1000 bp |
| Count | Number of sequences to generate. | 1 |
| Seed | Value to initialize the random generator. By default (seed = -1) the generator is initialized with the system time. | -1 |
| 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 |
| 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 |
| 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 |
| Reference | Path to the reference file (could be a sequence or an alignment). | |
| A | Adenine content. | 25% |
| C | Cytosine content. | 25% |
| G | Guanine content. | 25% |
| T | Thymine content. | 25% |
| 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 |
Parameters in Workflow File
Type: generate-dna
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| length | Lenght | numeric |
| count | Count | numeric |
| seed | Seed | numeric |
| content | Countent | string |
| algorithm | Algorithm | string Available values are:
|
| window-size | Window size | numeric |
| reference-url | Reference | string Available values are:
|
| percent-a | A | numeric |
| percent-c | C | numeric |
| percent-g | G | numeric |
| percent-t | T | numeric |
| gc-skew | 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 |