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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
  1. For varying values of the parameter fs_open_cost, the number of CDS pairs in the dataset is given.
  2. The values of the criteria for the reference method “needleprot” are indicated in italics characters. For each of the other methods (fse, fse0, macse_p, needlenuc), the variations of the criteria values as compared to the reference values are given. For each criteria and each method, the number of CDS pairs that have the closest value to the reference needleprot value is given in parentheses