Table 5.

Quality validation of programs for LTR retrotransposon prediction on the genome of D. melanogaster

Program used	LTR_STRUC	LTR_seq	LTR_Rho	LTR_FINDER	LTR harvest	LTR harvest	LTR_seq	LTR_Rho	LTR_FINDER	LTR harvest
Run-number	1	2	3	4-1	5-1	5-2	6	7	8	9
Parameter set	default*	default	default	default	default	default + clustering	see Tab. 1	see Tab.1	see Tab. 1	see Tab.1 + clustering
Index files contruction [s]	-	-	-	-	138	138	-	-	-	138
Run-time [s]	4380	24120	2286	1209	25	198**	1380	1709	320	170**
Annotations 'full length'	304	304	304	304	304	304	304	304	304	304
Predictions	310	188	417	395	723	490	160	398	204	411
Sensitivity	37.5%	36.8%	94.7%	74.3%	94.7%	97.4%	35.2%	96.1%	52.0%	97.7%
Specificity	36.8%	59.6%	69.1%	57.2%	40.4%	60.4%	66.9%	73.4%	77.5%	72.3%
Annotations 'all'	682	682	682	682	682	682	682	682	682	682
Predictions	310	188	417	395	723	490	160	398	204	411
Sensitivity	20.1%	22.0%	54.0%	45.9%	58.9%	57.9%	19.8%	53.5%	28.7%	56.3%
Specificity	44.2%	79.8%	88.2%	90.3%	55.6%	80.6%	84.4%	91.7%	96.1%	93.4%

* = parameters are not adjustable.

** = run-time LTRharvest + clustering with Vmatch.

Details on parameter settings and exact numbers of predictions are shown in Table C of the Additional file 1. Sensitivity and specificity values were calculated against the D. melanogaster annotation counting all TPs and hTPs as true positives.