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)
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