ORFmine
Overlap definition
Calculation of the overlap:
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An ORF is considered as overlapping a given genomic feature if the latter covers at least 70% of the ORF sequence.
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If less than 70% of an ORF sequence overlaps a genomic feature, but the latter is totally included in the ORF sequence, then the ORF is also considered as overlapping it.
Notice that the overlap threshold can be modified with the -co_ovp parameter. With the following instruction, an ORF is annotated as overlapping a given genomic feature if the latter covers at least 90% of the considered ORF.
orftrack -fna /database/genome.fasta -gff /database/genome.gff -co_ovp 0.90