Table 4 Values of the six criteria for the noFS dataset (variations as compared to needleprot)
From: Aligning coding sequences with frameshift extension penalties
fs_open_cost (# CDS pairs) | Method | Identity_NT | Identity_AA | Gap_init | Gap_length | FS_init | FS_length |
|---|---|---|---|---|---|---|---|
−10 (1672) | fse0 | 3281 (1158) | 5376 (1222) | −495 (1606) | −2718 (1521) | 0 (1672) | 0 (1672) |
fse | |||||||
macse_p | 8120 (955) | 27942 (676) | 3701 (711) | 9618 (1102) | 0 (1672) | 0 (1672) | |
needlenuc | 170239 (156) | −82002 (442) | 104811 (218) | 21422(427) | 44488 (256) | 263365 (256) | |
needleprot | 1090957 | 2047608 | 10230 | 530688 | 0 | 0 | |
−20 (3441) | fse0 | 1409 (2612) | −8622 (2672) | −3564 (3169) | −9984 (3057) | 0 (3441) | 0 (3441) |
fse | |||||||
macse_p | 24909 (1437) | 95844 (1011) | 13778 (1076) | 30884 (1791) | 0 (3441) | 0 (3441) | |
needleenuc | 547203 (176) | −177285 (680) | 317256 (219) | 52510 (552) | 138204 (257) | 844401 (257) | |
needleprot | 2000228 | 3494760 | 31793 | 1313658 | 0 | 0 | |
−30 (3740) | fse0 | 1368 (2834) | −10788 (2912) | −4047 (3448) | −11316 (3321) | 0 (3740) | 0 (3740) |
fse | |||||||
macse_p | 27840 (1547) | 106512 (1078) | 15561 (1117) | 34726 (1846) | 0 (3740) | 0 (3740) | |
needlenuc | 610305 (177) | −192231 (709) | 351748 (219) | 47356 (573) | 154255 (257) | 948418 (257) | |
needleprot | 2143630 | 3715632 | 35296 | 1439784 | 0 | 0 |