Table 4.

Quality validation of programs for LTR retrotransposon prediction on the genome of S. cerevisiae

Program used	LTR_STRUC	LTR_seq	LTR_Rho	LTR_FINDER	LTR harvest	LTR_seq	LTR_Rho	LTR_FINDER	LTR harvest
Run-number	1	2	3	4-1	5	6	7	8	9
Parameter set	default*	default	default	default	default	see Tab.1	see Tab.1	see Tab.1	see Tab.1
Index files contruction [s]	-	-	-	-	8	-	-	-	8
Run-time [s]	~600	413	190	19	3	126	168	19	2
Annotations	50	50	47	50	50	50	46	50	50
Predictions	39	50	46	56	68	38	38	43	45
Sensitivity	76%	80.0%	89.4%	100%	98.0%	74.0%	69.6%	84.0%	90.0%
Specificity	97.4%	100.0%	91.3%	89.3%	72.1%	97.4%	84.2%	97.7%	100%
Comment			program error chr03,06				program error chr03, 06,09

* = parameters are not adjustable.

Details on parameter settings and exact numbers of predictions are shown in Table B of the Additional file 1. Sensitivity and specificity values were calculated as outlined in the S. cerevisiae benchmark counting all TPs and hTPs as true positives. In run-no. 2 and no. 7, the program LTR_Rho reported an error for some chromosomal sequences. Thus the number of annotations and predictions was adjusted to the incomplete data set.