Table 5.

Evidentiary criteria for filtering transcript contigs based on the MAKER gene annotation features

	Annotation Tool	Annotation Call
Basis for Exclusion as lncRNA	blastx	protein_match
	genemark	match, match_part
	maker	CDS
	protein2genome	match_part, protein_match
	snap_masked	match, match_part
	tblastx	match_part, translated_nucleotide_match
not basis for Exclusion as lncRNA	blastn	expressed_sequence_match; match_part
	blastx	match_part
	cdna2genome	expressed_sequence_match; match_part
	est2genome	expressed_sequence_match; match_part
	maker	exon, gene, mRNA
	repeatmasker	match; match_part