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

Parameters in GUI

ParameterDescriptionDefault value
Annotate as (required)Name of the result annotations.ORF
Search inSpecifies which strands should be searched: direct, complement or both.both strands
Min lengthIgnores ORFs shorter than the specified length.100
Genetic codeSpecifies which genetic code should be used for translating the input nucleotide sequence.The Standard Genetic Code
Require init codonAllows or not ORFs starting with any codon other than terminator.True
Require stop codonIgnores boundary ORFs which last beyound the search region (i.e. have no stop codon within the range).False
Allow alternative codonsAllows ORFs starting with alternative initiation codons, accordingly to the current translation table.False

Parameters in Workflow File

Type: orf-search

ParameterParameter in the GUIType
result-nameAnnotate asstring
strandSearch in

numeric

Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
min-lengthMin lengthnumeric
genetic-codeGenetic code

string

Available values are:

  • NCBI-GenBank #1
  • NCBI-GenBank #2
  • etc.
require-init-codonRequire init codonboolean
require-stop-codonRequire stop codonboolean
allow-alternative-codonsAllow alternative codonsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence

And 1 output port:

Name in GUI: ORF annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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