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Table 4 Quality validation of programs for LTR retrotransposon prediction on the genome of S. cerevisiae

From: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

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   
  1. * = parameters are not adjustable.
  2. 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.