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The element searches for open reading frames (ORFs) in the supplied sequence.

Parameters in GUI

ParameterDescriptionDefault value
Annotate AsName of the result annotations.ORF
DirectionSee the description here.Any
Allow alternative codonsAllows / disallows ORFs starting with alternative initiation codons, accordingly to the current translation table.False
Require init codonsAllows / disallows ORFs starting with any codon other than terminator.True
Require stop codonsIgnores or takes into account boundary ORFs which last beyond the search region.False
Min lengthIgnores ORFs shorter than the specified length.100bp
Max lengthMaximum length of annotation allowed.10000bp
Genetic codeGenetic code that should be used to translate the input nucleotide sequence.The standard genetic code

 

Parameters in Schema File

Type: orf

ParameterParameter in the GUIType
keyAnnotate Asstring
strandDirection

string

Available values are:

  • complement
  • direct
  • both
alt-startAllow alternative codonsboolean
starts-with-initRequire init codonsboolean
ends-with-stopRequire stop codonsboolean
min-lengthMin lengthnumeric
max-lengthMax lengthnumeric
trans-idGenetic code

string

Available values are:

  • “NCBI-GenBank #1”
  • “NCBI-GenBank #2”
  • etc.
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