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Table 5 Quality validation of programs for LTR retrotransposon prediction on the genome of D. melanogaster

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 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%
  1. * = parameters are not adjustable.
  2. ** = run-time LTRharvest + clustering with Vmatch.
  3. 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.