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Generates random DNA sequences with given nucleotide content that can be specified manually or evaluated from the reference file.

Parameters in GUI

ParameterDescriptionDefault value
LengthLength of the resulted sequence or sequences.1000 bp
CountNumber of sequences to generate.1
SeedValue to initialize the random generator. By default (seed = -1) the generator is initialized with the system time.-1
ContentSpecifies 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
AlgorithmAlgorithm for generating random sequence(s). Two algorithms are available: GC Content and GC Skew. If you choose GC Content, then parameters A,CGT are used to generate the sequence. Otherwise, the GC Skewparameter is used to generate the sequence(s).GC Content
Window sizeThe DNA sequence generation is divided into windows of the specified size. In each window the bases ratio, defined by other parameters, is kept.1000
ReferencePath to the reference file (could be a sequence or an alignment). 
AAdenine content.25%
CCytosine content.25%
GGuanine content.25%
TThymine content.25%
GC SkewGC 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

ParameterParameter in the GUIType
lengthLenghtnumeric
countCountnumeric
seedSeednumeric
contentCountentstring
algorithmAlgorithm

string

Available values are:

  • gc-content
  • gc-skew
window-sizeWindow sizenumeric
reference-urlReference

string

Available values are:

  • manual
  • reference
percent-aAnumeric
percent-cCnumeric
percent-gGnumeric
percent-tTnumeric
gc-skewGC Skewnumeric

Input/Output Ports

The element has 1 output port:

Name in GUI: Sequences

Name in Workflow File: out-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence
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