Table 3.

CDS/intron classification by UFM with filters 1, 2 and 3 in CDS and intron sequences of H. sapiens, D. melanogaster and A. thaliana varying between 150 and 400 bp.

Species	Filters	Seq.	Size, bp
			150	200	250	300	350	400
H. sapiens	0	CDS*	100	100	100	100	100	100
		Intron**	57.7	40.6	27.5	20.5	15	11.7
	1	CDS	96.5	96.9	97.5	97.8	98.4	98.9
		Intron	47.0	29.8	17.1	10.5	7.0	4.2***
	1 + 3	CDS	85.3	87.9	89.2	92.6	93.5	94.5
		Intron	28.4	18.3	10.7	7.6	4.8	2.7
	2 + 3	CDS	78.1	81.0	82.6	85.0	86.5	87.8
		Intron	20.3	11.0	4.6	3.3	1.5	0.8
D. melanogaster	0	CDS	100	99.8	100	99.9	99.9	99.9
		Intron	43.6	25.8	12.2	5.6	3.7	2.6
	1	CDS	97.7	98.3	98.7	98.5	98.6	98.8
		Intron	43.6	25.8	12.2	5.6	3.7	2.6
	1 + 3	CDS	87.2	89.7	90.9	92.3	93.4	94.1
		Intron	25.6	13.2	8.4	3.9	2.3	1.8
	2 + 3	CDS	81.3	82.2	83.6	86.0	87.4	88.5
		Intron	21.5	11.5	5.8	3.1	1.8	1.4
A. thaliana	0	CDS	99.7	99.8	99.9	100	99.8	99.9
		Intron	27.1	9.1	2.6	0.8	0	0
	1	CDS	99.7	99.7	99.8	100	99.8	99.9
		Intron	27.1	9.1	2.6	0.8	0	0
	1 + 3	CDS	86.9	88.3	90.9	92.7	94	94.4
		Intron	16.2	5.3	1.8	0.7	0	0
	2 + 3	CDS	76.2	77.0	79.3	83.2	85.3	85.9
		Intron	16.2	5.3	1.8	0.7	0	0

^*“CDS” indicates the proportion (%) of CDS that were correctly classified by the corresponding algorithm, i.e. the true positives. The CDS that are not detected, i.e. the false negatives are missing from the CDS output list.

^**“Intron” indicates the proportion (%) of introns that were wrongly classified, i.e. the false positives. The non-coding sequences correctly classified do not appear in the output list. All entries whose values is >0 contain an ORF whose purine bias is typical of a CDS for the size threshold considered.

^***Gray areas indicate cases where the false positive rate of coding ORF diagnosis is below or close to 5%.