ORF definition#

ORFs are defined according to the recent definition proposed by Sieber et al, in 2018.

An ORF:

  • has a length divisible by 3
  • is bounded by stop codons
  • is at least 60 nucleotides long (STOP codons excluded)

orf_definition

The minimal length of an ORF can be nevertheless modified by the user with the -orf_len parameter (notice that the ORF length does not include the STOP codons). The following instruction extracts all ORFs of at least 100 amino acids: 

orftrack -fna /database/genome.fasta -gff /database/genome.gff -orf_len 300