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Generates random DNA sequences wi= th given nucleotide content that can be specified manually or evaluated fro= m the reference file.
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 def= ault (seed =3D -1) the generator is initialized with the system time. | -1 |
Content | Specifies how the nucleotide content of the sequ= ence(s) should be generated. It can be either taken from the reference file= (see the Referenceparameter), or input ma= nually. | 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<=
/em> 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 wind= ows 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), wher= e G is the number of G=E2=80=99s in the window, and C is the number of C=E2= =80=99s. | 0.25 |
Parameters in = Workflow File
Type: generate-dna<= /p>
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= span>
The element has 1 output port:
Name in GUI: Sequences
Name in Workflow&nbs= p;File: out-sequence
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Sequence | sequence | sequence |