Skip to main content

Table 2 Detection performance of HMMs

From: Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Name M Organism Chromosome Threshold Detected ( n) Missed ( n) Additional positive ( n) Sensitivity (%)
Zama 290 Drosophila melanogaster 3L 23 6 (13) 4 (1) 80 (84) 60 (93)
Anopheles gambiae 2R
Mag Cb 50 Anopheles gambiae 2R 14 0 (0) 0 (12) 155 NA (0)
Mag A 90 Anopheles gambiae 2R 20 3 (25) 1 (34) 36 75 (42)
CsRN1 90 Anopheles gambiae 2R 12 1 (31) 0 (11) 117 100 (74)
Sushi 270 Danio rerio 7 35 8 (46) 24 (78) 122 25 (37)
rGmr1 150 Danio rerio 7 20 7 (35) 78 (260) 38 8 (12)
Sire 150 Oryza sativa 1 20 3 (10) 1 (3) 53 75 (77)
Retrofit 150 Oryza sativa 1 35 4 (8) 2 (2) 4 67 (80)
  1. The detection performance was not extensively evaluated. The number of LTRs detected in one chromosome of a suitable eukaryotic organism, the number of LTRs missed and the number of additional positives as compared to the RepeatMasker output for the chosen chromosome are shown. The threshold, number of match states M and sensitivity are also tabulated. Two numbers for the sensitivity are reported, first the sensitivity for LTRs not belonging to the training set and second the sensitivity for all LTRs in the clade of interest between parentheses.
  2. aTwo chromosomes from different organisms were screened.
  3. bAll LTRs in the clade belonged to the training set.