Table 5 Values of the six criteria for the FS dataset
From: Aligning coding sequences with frameshift extension penalties
fs_open_ cost | fs_extend_cost (# CDS pairs) | Method | Identity_ NT | Identity_ AA | Gap_ init | Gap_ length | FS_init (avg) | FS_ length |
|---|---|---|---|---|---|---|---|---|
−10 | −1 (212) | fse0 | 166002 | 325212 | 895 | 60662 | 226 (1.06 ± 0.25) | 20219 |
fse | 165720 | 325026 | 901 | 60624 | 216 (1.01 ± 0.14) | 18705 | ||
macse_p | 166167 | 324999 | 1445 | 61562 | 432 (2.03 ± 3.06) | 22742 | ||
needlenuc | 172959 | 321348 | 5053 | 60038 | 2103 (9.91 ± 26.73) | 29616 | ||
−0.5 (386) | fse0 | 252590 | 464712 | 2400 | 114859 | 482 (1.24 ± 0.47) | 31777 | |
fse | 251647 | 463407 | 2387 | 115269 | 401 (1.03 ± 0.19) | 26982 | ||
macse_p | 253715 | 465594 | 4161 | 117165 | 1306 (3.38 ± 4.53) | 41742 | ||
needlenuc | 279682 | 452673 | 19408 | 113195 | 8032 (20.80 ± 31.02) | 68226 | ||
−0.2 (619) | fse0 | 371062 | 641748 | 5334 | 204370 | 805 (1.30 ± 0.52) | 43381 | |
fse | 370260 | 640377 | 5270 | 204806 | 688 (1.11 ± 0.33) | 37376 | ||
macse_p | 374729 | 646893 | 9308 | 208344 | 2893 (4.67 ± 5.34) | 72030 | ||
needlenuc | 442564 | 618270 | 48799 | 209420 | 19751 (31.90 ± 34.48) | 141217 | ||
−20 | −1 (161) | fse0 | 123814 | 244350 | 461 | 40315 | 168 (1.04 ± 0.20) | 17770 |
fse | 123610 | 244149 | 468 | 40195 | 164 (1.01 ± 0.14) | 16924 | ||
macse_p | 123541 | 243591 | 709 | 40585 | 223 (1.38 ± 1.03) | 18119 | ||
needlenuc | 125452 | 242742 | 1493 | 39031 | 650 (4.03 ± 5.85) | 19405 | ||
−0.5 (189) | fse0 | 147476 | 291147 | 549 | 49485 | 197 (1.04 ± 0.20) | 19599 | |
fse | 147401 | 291048 | 557 | 49363 | 194 (1.02 ± 0.16 ) | 19279 | ||
macse_p | 147143 | 290271 | 838 | 49841 | 260 (1.37 ± 0.98) | 19976 | ||
needlenuc | 149551 | 289086 | 1872 | 47515 | 808 (4.27 ± 6.17) | 21440 | ||
−0.2 (216) | fse0 | 161906 | 318117 | 723 | 55383 | 225 (1.04 ± 0.20) | 21300 | |
fse | 161865 | 318099 | 732 | 55393 | 223 ( 1.03 ± 0.18) | 21115 | ||
macse_p | 161622 | 317205 | 1061 | 55715 | 306 (1.41 ± 0.99) | 21997 | ||
needlenuc | 165260 | 315531 | 2851 | 53613 | 1186 (5.49 ± 6.82) | 24403 | ||
−30 | −1 (71) | fse0 | 47071 | 91266 | 230 | 26303 | 76 (1.07 ± 0.26) | 12845 |
fse | 46872 | 91032 | 233 | 26183 | 72 (1.01 ± 0.12) | 12302 | ||
macse_p | 46936 | 90876 | 372 | 26325 | 118 (1.66 ± 1.25) | 13142 | ||
needlenuc | 48290 | 91017 | 866 | 26135 | 391 (5.50 ± 5.67) | 13829 | ||
−0.5 (154) | fse0 | 120558 | 237768 | 445 | 37975 | 159 (1.03 ± 0.18) | 17554 | |
fse | 120504 | 237678 | 452 | 37851 | 157 (1.01 ± 0.14) | 17319 | ||
macse_p | 120338 | 237084 | 691 | 38047 | 212 (1.37 ± 1.00) | 17926 | ||
needlenuc | 122084 | 236904 | 1321 | 37531 | 575 (3.73 ± 5.14) | 18877 | ||
−0.2 (178) | fse0 | 137451 | 271041 | 525 | 46049 | 184 (1.03 ± 0.18) | 18995 | |
fse | 137440 | 271008 | 531 | 45917 | 183 (1.02 ± 0.17) | 18872 | ||
macse_p | 137175 | 270258 | 803 | 46187 | 244 ( 1.37 ± 0.97) | 19395 | ||
needlenuc | 139489 | 269139 | 1803 | 44303 | 779 (4.38 ± 6.27) | 20859 |