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 |