Table 2 Amount of sequences extracted by classification and amount of duplicated sequences eliminated during the preprocessing
From: Transductive learning as an alternative to translation initiation site identification
Downstream | TIS | UPSTREAM | UPSTREAM | CDS | CDS | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Window | out of Phase (nTIS) | in Phase | in Phase | out of Phase | |||||||
Non-duplicated | Duplicated | Non-duplicated | Duplicated | Non-duplicated | Duplicated | Non-duplicated | Duplicated | Non-duplicated | Duplicated | ||
Rattus norvegicus | |||||||||||
235 | 113 | 49 | 123 | 61 | 58 | 34 | 11703 | 1373 | 9738 | 1989 | |
518 | 100 | 38 | 124 | 47 | 60 | 29 | 8630 | 1120 | 6161 | 1638 | |
800 | 81 | 29 | 114 | 41 | 58 | 28 | 2141 | 945 | 2170 | 1451 | |
1081 | 66 | 22 | 101 | 39 | 57 | 24 | 546 | 824 | 983 | 1278 | |
1365 | 48 | 14 | 86 | 37 | 54 | 15 | 463 | 741 | 822 | 1158 | |
1650 | 42 | 11 | 69 | 28 | 40 | 11 | 420 | 675 | 720 | 1056 | |
Mus musculus | |||||||||||
235 | 678 | 358 | 776 | 471 | 308 | 170 | 5154 | 4853 | 8364 | 8067 | |
518 | 581 | 272 | 810 | 384 | 315 | 147 | 4323 | 3779 | 7230 | 6316 | |
800 | 466 | 203 | 726 | 331 | 288 | 127 | 3612 | 2927 | 6102 | 5000 | |
1081 | 398 | 158 | 632 | 293 | 260 | 113 | 2976 | 2311 | 5318 | 3931 | |
1365 | 319 | 113 | 568 | 234 | 242 | 92 | 2506 | 1839 | 4440 | 3124 | |
1650 | 277 | 79 | 495 | 187 | 208 | 68 | 2104 | 1463 | 3757 | 2454 | |
Homo sapiens | |||||||||||
235 | 13564 | 7271 | 17729 | 9177 | 6972 | 3386 | 109658 | 109137 | 194726 | 192024 | |
518 | 13124 | 5674 | 18760 | 7188 | 7606 | 2492 | 94503 | 83527 | 171463 | 150192 | |
800 | 11579 | 4398 | 17917 | 5914 | 7334 | 1986 | 79368 | 63663 | 148148 | 117440 | |
1081 | 9716 | 3366 | 16085 | 4902 | 6629 | 1677 | 65717 | 48341 | 126260 | 90786 | |
1365 | 7753 | 2469 | 13662 | 3853 | 5649 | 1371 | 54818 | 37422 | 106842 | 71030 | |
1650 | 5877 | 1793 | 10918 | 2871 | 4537 | 1098 | 46233 | 29136 | 91066 | 56808 | |
Drosophila melanogaster | |||||||||||
235 | 15225 | 10455 | 26777 | 18065 | 12378 | 8252 | 142022 | 194250 | 200046 | 285816 | |
518 | 13723 | 9076 | 27548 | 16202 | 12787 | 7432 | 119185 | 162288 | 171884 | 244359 | |
800 | 11942 | 7745 | 26905 | 14748 | 12581 | 6704 | 99615 | 134106 | 146638 | 208787 | |
1081 | 10122 | 6594 | 25725 | 13314 | 12086 | 6092 | 82645 | 110225 | 124842 | 178443 | |
1365 | 8344 | 5400 | 23695 | 11929 | 11233 | 5474 | 69079 | 91113 | 106093 | 153047 | |
1650 | 6657 | 4390 | 21482 | 10472 | 10227 | 4740 | 58253 | 75705 | 90979 | 131754 | |
Arabidopsis thaliana | |||||||||||
235 | 20867 | 5157 | 15869 | 3515 | 6542 | 1319 | 196447 | 56135 | 388223 | 116238 | |
518 | 18440 | 9200 | 15663 | 2677 | 6555 | 975 | 145585 | 38519 | 299284 | 82624 | |
800 | 14948 | 3013 | 14112 | 2122 | 5968 | 750 | 105415 | 25929 | 221892 | 56195 | |
1081 | 11082 | 2046 | 11644 | 1592 | 4942 | 562 | 74236 | 17100 | 160512 | 38259 | |
1365 | 7683 | 1281 | 8453 | 1112 | 3658 | 399 | 51462 | 11625 | 115329 | 26194 | |
1650 | 4967 | 839 | 5952 | 808 | 2582 | 283 | 36505 | 8297 | 83812 | 18706 | |