Table 1 Comparisons of the performances of RepeatScout, ReCon, WindowMasker, and Red. Repeats detected by RepeatMasker are considered the ground truth in this study
From: Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
SN te | SN tr | SN low | SN other | SN all | SP exon | PP | FPL | PR | Time | Memory | |
|---|---|---|---|---|---|---|---|---|---|---|---|
Tool | (%) | (%) | (%) | (%) | (%) | (%) | (%) | (bp) | (bp) | (sec) | (MB) |
Homo sapiens– 3,099,750,718 bp | |||||||||||
RS | 62.5 | 79.6 | 13.6 | 29.2 | 63.5 | 90.5 | 33.7 | 239474 | 9355324a | 948,350 | 4701 |
Red | 61.0 | 86.2 | 68.9 | 33.9 | 62.8 | 89.3 | 35.5 | 2657024 | 16414125a | 5184 | 6775 |
WM | 55.2 | 74.9 | 81.9 | 25.7 | 56.7 | 87.2 | 36.1 | 423707488 | 3109241a | 14866 | 615 |
RC | 55.0 | 75.2 | 11.0 | 11.5 | 56.2 | 95.4 | 29.2 | 137633 | 3575640a | 898,844 | 14666 |
Drosophila melanogaster– 143,726,002 bp | |||||||||||
Red | 90.0 | 59.4 | 43.3 | 83.0 | 84.1 | 94.0 | 23.2 | 312686 | 9401953 | 206 | 916 |
RS | 86.3 | 24.3 | 1.9 | 71.8 | 74.4 | 98.0 | 18.4 | 0 | 4913141 | 79008 | 979 |
RC | 86.7 | 18.2 | 1.8 | 80.0 | 74.0 | 99.0 | 17.6 | 0 | 4002422 | 13979 | 1513 |
WM | 45.5 | 64.8 | 62.7 | 42.1 | 48.8 | 90.8 | 22.3 | 15150087 | 17118084 | 2869 | 325 |
Zea mays– 2,059,943,587 bp | |||||||||||
RS | 96.7 | 55.5 | 25.8 | 89.9 | 96.3 | – | 80.0 | 44447 | 66587503 | 347082 | 7344 |
Red | 93.3 | 58.1 | 31.9 | 88.7 | 93.0 | – | 78.8 | 6257 | 94687287 | 2731 | 6741 |
RC | 91.6 | 33.5 | 12.9 | 88.8 | 91.1 | – | 74.3 | 20864 | 32450624 | 192223 | 3419 |
WM | 82.3 | 63.7 | 40.1 | 86.6 | 82.1 | – | 67.2 | 36189699 | 33998795 | 7589 | 639 |
Glycine max– 973,344,380 bp | |||||||||||
RC | 96.3 | 42.5 | 22.6 | 99.9 | 92.7 | 95.1 | 46.4 | 2144642 | 123719267 | 304490 | 8609 |
RS | 92.5 | 39.6 | 19.1 | 94.4 | 89.0 | 92.0 | 43.6 | 2690420 | 110068092 | 134936 | 1516 |
Red | 86.9 | 42.5 | 28.9 | 96.1 | 83.9 | 94.5 | 41.6 | 1794609 | 107704170 | 1653 | 1770 |
WM | 68.1 | 83.4 | 83.6 | 3.5 | 68.9 | 95.4 | 44.4 | 170352943 | 186081334 | 13319 | 356 |
Dictyostelium discoideum– 34,121,699 bp | |||||||||||
Red | 94.7 | 93.8 | 96.5 | 1.0 | 94.3 | – | 54.9 | 2378281 | 10582912 | 61 | 235 |
WM | 35.1 | 92.7 | 95.1 | 4.8 | 84.7 | – | 53.0 | 14238455 | 10769264 | 20 | 2 |
RC | 95.0 | 25.0 | 7.6 | 0.0 | 31.9 | – | 13.6 | 0 | 1883829 | 18317 | 957 |
RS | 79.4 | 27.0 | 4.6 | 0.0 | 30.4 | – | 13.5 | 0 | 1969788 | 17476 | 925 |
Plasmodium falciparum– 23,264,338 bp | |||||||||||
WM | – | 91.2 | 90.6 | 28.5 | 89.2 | – | 61.4 | 10902380 | 10246592 | 23 | 7 |
Red | – | 87.6 | 84.2 | 90.7 | 87.2 | – | 51.8 | 972553 | 8129833 | 63 | 416 |
RS | – | 43.9 | 9.9 | 40.1 | 39.4 | – | 15.3 | 36882 | 1797419 | 36194 | 918 |
RC | – | 20.3 | 7.7 | 34.5 | 19.1 | – | 9.3 | 4827 | 1314829 | 7011 | 1052 |
Mycobacterium tuberculosis– 4,403,837 bp | |||||||||||
Red | – | 88.7 | 81.0 | – | 88.5 | – | 44.0 | 160705 | 1914667 | 7 | 1 |
WM | – | 63.6 | 33.3 | – | 63.0 | – | 17.5 | 672523 | 755248 | 2 | 2 |
RS | – | 20.8 | 27.3 | – | 21.0 | – | 5.6 | 0 | 240852 | 331 | 640 |
RC | – | 0.0 | 0.0 | – | 0.0 | – | 0.0 | 0 | 2089 | 69 | 852 |