Table 1.
Improvement of RAIDER over RepeatScout as measured by masking-based sensitivity, as well as RepeatMasker-based sensitivity
| Seed | Organism | Simulation | Simulation | Masking | RM-based | phRaider | RptScout | Speedup |
|---|---|---|---|---|---|---|---|---|
| index | basis | size | Sensitivity | Sensitivity | runtime | runtime | ||
| (Mb) | (v. RS) | (v. RS) | (seconds) | (seconds) | ||||
| Seeds selected to optimize Masking Sensitivity | ||||||||
| 537 | arabidopsis | chr5 | 2.91 | 0.51 | 0.06 | 1 | 26 | 260 |
| 516 | C. elegans | chrI | 4.01 | 0.11 | −0.11 | 1 | 120 | 1201 |
| 545 | C. elegans | chrII | 3.18 | 0.12 | −0.04 | 2 | 73 | 730 |
| 489 | C. elegans | chrIII | 3.75 | 0.11 | −0.13 | 1 | 114 | 1143 |
| 536 | C. elegans | chrIV | 3.63 | 0.11 | −0.09 | 1 | 117 | 1179 |
| 480 | C. elegans | chrV | 4.90 | 0.14 | −0.02 | 1 | 252 | 2522 |
| 512 | human | chr22 | 22.94 | 0.04 | −0.02 | 41 | 474 | 114 |
| 545 | mouse | chr19 | 32.15 | 0.01 | −0.05 | 47 | 2319 | 491 |
| Seeds selected to optimize RepeatMasker sensitivity | ||||||||
| 537 | arabidopsis | chr5 | 2.99 | 0.08 | 0.06 | 1 | 26 | 260 |
| 154 | C. elegans | chrII | 3.21 | 0.08 | −0.02 | 1 | 73 | 730 |
| 154 | C. elegans | chrIV | 3.66 | 0.07 | −0.05 | 1 | 117 | 1175 |
| 70 | C. elegans | chrIII | 3.75 | 0.04 | −0.1 | 1 | 114 | 114 |
| 262 | C. elegans | chrI | 4.03 | 0.08 | −0.09 | 1 | 120 | 1209 |
| 262 | C. elegans | chrV | 4.90 | 0.12 | 0.01 | 1 | 252 | 2521 |
| 508 | human | chr22 | 37.96 | 0.04 | −0.01 | 29 | 474 | 164 |
| 262 | mouse | chr19 | 42.25 | −0.02 | −0.04 | 57 | 2319 | 401 |
| 537 | human | chr18 | 43.11 | 0.03 | −0.07 | 71 | 1412 | 191 |
| Single seed picked for balance on all organisms | ||||||||
| 262 | arabidopsis | chr5 | 2.99 | 0.04 | 0.04 | 1 | 26 | 260 |
| 262 | C. elegans | chrII | 3.21 | 0.1 | −0.02 | 1 | 73 | 730 |
| 262 | C. elegans | chrIV | 3.66 | 0.08 | −0.06 | 1 | 117 | 1176 |
| 262 | C. elegans | chrIII | 3.75 | 0.08 | −0.11 | 1 | 114 | 1141 |
| 262 | C. elegans | chrI | 4.03 | 0.08 | −0.09 | 1 | 120 | 1209 |
| 262 | C. elegans | chrV | 4.90 | 0.12 | 0.01 | 1 | 252 | 2521 |
| 262 | human | chr22 | 37.96 | 0.03 | −0.02 | 37 | 474 | 124 |
| 262 | human | chr18 | 42.25 | 0.01 | −0.08 | 85 | 1412 | 161 |
| 262 | mouse | chr19 | 43.11 | −0.02 | −0.04 | 57 | 2319 | 401 |
Specificity is near identical (≥98%) in all cases. The seed index is an arbitrarily assigned index of the seed (see Supplementary appendix). Seeds were chosen by using the best from a small random sampling over a range of weights and lengths.