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

Element type: generate-dna


ParameterDescriptionDefault valueParameter in Workflow FileType
LengthLength of the resulted sequence or sequences.1000 bplengthnumeric
CountNumber of sequences to generate.1countnumeric
SeedValue to initialize the random generator. By default (seed = -1) the generator is initialized with the system time.-1seednumeric
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.manualcontentstring
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 Contentalgorithm


Available values are:

  • gc-content
  • gc-skew
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.1000window-sizenumeric
ReferencePath to the reference file (could be a sequence or an alignment).


Available values are:

  • manual
  • reference
AAdenine content.25%percent-anumeric
CCytosine content.25%percent-cnumeric
GGuanine content.25%percent-gnumeric
TThymine content.25%percent-tnumeric
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.0.25gc-skewnumeric

Input/Output Ports

The element has 1 output port:

Name in GUI: Sequences

Name in Workflow File: out-sequence


Slot In GUISlot in Workflow FileType