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Finds Open Reading Frames (ORFs) in each supplied nucleotide sequence, stores found regions as annotations.

Element type: orf-search

Parameters in GUI

ParameterDescriptionDefault valueParameter in Workflow FileType
Annotate as (required)Name of the result annotations.ORFresult-namestring
Search inSpecifies which strands should be searched: direct, complement or both.both strandsstrand


Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
Min lengthIgnores ORFs shorter than the specified length.100min-lengthnumeric
Genetic codeSpecifies which genetic code should be used for translating the input nucleotide sequence.The Standard Genetic Codegenetic-code


Available values are:

  • NCBI-GenBank #1
  • NCBI-GenBank #2
  • etc.
Require init codonAllows or not ORFs starting with any codon other than terminator.Truerequire-init-codonboolean
Require stop codonIgnores boundary ORFs which last beyound the search region (i.e. have no stop codon within the range).Falserequire-stop-codonboolean
Allow alternative codonsAllows ORFs starting with alternative initiation codons, accordingly to the current translation table.Falseallow-alternative-codonsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence


Slot In GUISlot in Workflow FileType

And 1 output port:

Name in GUI: ORF annotations

Name in Workflow File: out-annotations


Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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