Table 1.
Promoter prediction in 48 different eukaryotes.
| Genome size in Mb | Genome GC % | Promoter sequences | Total predictions | TP predictions | TP genes | Recall | |
|---|---|---|---|---|---|---|---|
| Yeast | |||||||
| S. cerevisiae | 12.5 | 38.4 | 6642 | 8113 | 6636 | 5386 | 81.1 |
| S. bayanus | 11.9 | 40.3 | 7216 | 8161 | 6415 | 5346 | 74.1 |
| S. castellii | 11.4 | 37 | 4655 | 5745 | 4528 | 3703 | 79.5 |
| S. kluyveri | 11 | 41.7 | 2932 | 2991 | 2433 | 2059 | 70.2 |
| S. kudriazvevii | 11.2 | 39.9 | 3736 | 4157 | 3431 | 2863 | 76.6 |
| S. mikatae | 10.8 | 38.2 | 3064 | 3773 | 3054 | 2465 | 80.5 |
| S. paradoxus | 11.9 | 38.6 | 7373 | 8578 | 6807 | 5608 | 76.1 |
| C. albicans | 14.5 | 33.7 | 5852 | 8628 | 6764 | 5063 | 86.5 |
| C. dubliniensis | 14.6 | 33.2 | 5933 | 8988 | 7114 | 5255 | 88.6 |
| C. glabrata | 12.1 | 38.5 | 5149 | 6913 | 5913 | 4575 | 88.9 |
| C. lusitaniae | 12.1 | 44.5 | 5797 | 5621 | 4867 | 4051 | 69.9 |
| C. tropicalis | 15.3 | 33.5 | 6119 | 8855 | 6714 | 5112 | 83.5 |
| D. hansenii | 11.5 | 35.4 | 6102 | 9100 | 7459 | 5592 | 91.6 |
| L. elongisporus | 15.5 | 37 | 5657 | 8337 | 6933 | 5076 | 89.7 |
| Worm | |||||||
| C. elegans | 98.3 | 35.4 | 32481 | 49575 | 34895 | 26474 | 81.5 |
| C. brenneri | 190.4 | 39.7 | 24989 | 28345 | 19993 | 16714 | 66.9 |
| C. briggsae | 108.4 | 37.7 | 31342 | 36290 | 25460 | 21187 | 67.6 |
| C. remanei | 145.4 | 38.5 | 26174 | 30728 | 21571 | 17874 | 68.3 |
| C. japonica | 166.3 | 39.9 | 22173 | 28033 | 19710 | 16061 | 72.4 |
| Fly | |||||||
| D. melanogaster | 143.7 | 42.1 | 17283 | 24152 | 18720 | 14536 | 84.1 |
| D. annanassae | 231 | 42.5 | 13677 | 18831 | 12513 | 10127 | 74.0 |
| D. erecta | 152.7 | 42.6 | 12395 | 15917 | 10887 | 8996 | 72.6 |
| D. grimshawi | 200.5 | 38.8 | 7861 | 10009 | 6822 | 5498 | 69.9 |
| D. mojavensis | 193.8 | 40.2 | 5329 | 7172 | 4982 | 3885 | 72.9 |
| D. persimilis | 188.4 | 45.2 | 7598 | 10487 | 7452 | 5812 | 76.5 |
| D. pseudoobscura | 152.7 | 45.3 | 31482 | 45081 | 32400 | 25117 | 79.8 |
| D. sechellia | 166.6 | 42.5 | 19059 | 25110 | 17308 | 13974 | 73.3 |
| D. virilis | 206 | 40.7 | 7920 | 10433 | 7238 | 5673 | 71.6 |
| D. yakuba | 165.7 | 42.4 | 2857 | 3951 | 2619 | 2105 | 73.7 |
| A. gambiae | 265 | 44.5 | 13901 | 17893 | 13044 | 10487 | 75.4 |
| A. mellifera | 250.3 | 34.1 | 21146 | 36526 | 23533 | 17690 | 83.7 |
| Marine invertebrates | |||||||
| Sea hare | 927.3 | 42 | 33340 | 41949 | 28465 | 23737 | 71.2 |
| Sea squirt | 116.7 | 36.1 | 729 | 1073 | 748 | 591 | 81.1 |
| Lancelet | 521.9 | 41.8 | 30538 | 41175 | 27789 | 23402 | 76.6 |
| Fishes | |||||||
| Zebrafish | 1371.7 | 36.7 | 14404 | 20036 | 13780 | 11329 | 78.7 |
| Fugu | 391.5 | 45.8 | 18679 | 25638 | 17793 | 14685 | 78.6 |
| Lamprey | 885.5 | 46.8 | 8724 | 11355 | 8087 | 6839 | 78.4 |
| Medaka | 869.8 | 42.3 | 29255 | 40229 | 27999 | 23106 | 79.0 |
| Stickleback | 446.6 | 42 | 38971 | 54946 | 37856 | 30987 | 79.5 |
| Tetraodon | 342.4 | 46.3 | 34618 | 50425 | 34481 | 27838 | 80.4 |
| Mammals and bird | |||||||
| Mouse | 2803.6 | 41.9 | 23878 | 34040 | 23118 | 18661 | 78.2 |
| Human | 2851.4 | 40.9 | 26800 | 41102 | 27229 | 21419 | 79.9 |
| Chicken | 1046.9 | 41.9 | 3707 | 5292 | 3353 | 2753 | 74.3 |
| Cow | 2983.3 | 42.3 | 7514 | 11110 | 7338 | 5849 | 77.8 |
| Elephant | 3196.7 | 40.9 | 16095 | 22427 | 15638 | 12580 | 78.2 |
| Pig | 2808.5 | 42.5 | 11953 | 18064 | 12403 | 9736 | 81.5 |
| Platypus | 1995.6 | 45.7 | 6166 | 8336 | 5969 | 4735 | 76.8 |
| Rat | 2616.4 | 42.4 | 8567 | 11987 | 8498 | 6817 | 79.6 |
Promoter prediction in 14 species of yeast, five species of worm, 12 species of fly, three marine invertebrates, six fish species, seven mammals and chicken are carried out using PromPredict algorithm. The promoter regions, −500 to +500 relative to TLS (TLS at 0) are considered for this analysis and are retrieved from SGD, CGD, and UCSC genome browsers. The −500 to +100 relative to TLS is considered as true positive region.