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Table 6 Values of the six criteria for the ambiguFS 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 (2127) fse0 (862) 1095102 1737105 24489 908218 1111 (1.28 ± 0.54) 42730
fse 1086546 1719774 23483 906540 0 0
macse_p (2076) 1124316 1790199 45335 936002 12436 (5.99 \(\pm\,4.96\)) 216772
needleprot 1085007 1723950 25288 916518 0 0
−0.5 (1953) fse0 (688) 1008514 1597605 22984 854021 855 (1.24 \(\pm\,0.53\) ) 31172
fse (2) 1003293 1587258 22102 853793 2 (1.0 \(\pm\,0\) ) 80
macse_p (1902) 1036768 1649604 42619 880399 11562 (6.07 \(\pm\,4.91\)) 197772
needleprot 1001957 1591134 23790 863199 0 0
−0.2 (1720) fse0 (455) 890042 1420569 20050 764510 532 (1.16 \(\pm\,0.48\)) 19568
fse (3) 887372 1415403 19465 764162 3 (1.0 \(\pm\,0\)) 92
macse_p (1669) 915754 1468305 37472 789220 9975 (5.97 \(\pm\,4.75\)) 167484
needleprot 886178 1418748 20955 772272 0 0
−20 −1 (409) fse0 (100) 219277 358554 3633 153487 120 (1.2 \(\pm\,0.40\)) 6937
fse 216936 353586 3619 152391 0 0
macse_p (403) 225976 374391 6509 158165 1348 (3.34 \(\pm\,3.00\)) 36179
needleprot 216842 355656 4172 153957 0 0
−0.5 (381) fse0 (72) 195615 311757 3545 144317 91 (1.26 \(\pm\,0.44\)) 5108
fse 194048 308448 3505 144045 0 0
macse_p (375) 202374 327711 6380 148909 1311 (3.49 \(\pm\,3.05\)) 34322
needleprot 193980 310632 4051 145563 0 0
−0.2 (354) fse0 (45) 181185 284787 3371 138419 63 (1.4 \(\pm\,0.49\)) 3407
fse (1) 180151 282693 3344 138217 1 (1.0 \(\pm\,0\)) 40
macse_p (348) 187895 300777 6157 143035 1265 (3.63 \(\pm\,3.11\)) 32301
needleprot 180116 284946 3883 139731 0 0
−30 −1 (200) fse0 (119) 151090 289617 805 42437 120 (1.01 \(\pm\,0.09\)) 6818
fse 147590 282018 852 40221 0 0
macse_p (200) 152626 292254 1309 43043 378 (1.89 \(\pm\,2.16\)) 14515
needleprot 147228 281472 933 40455 0 0
−0.5 (117) fse0 (36) 77603 143115 590 30765 37 (1.02 \(\pm\,0.16\)) 2109
fse 76678 141108 626 29913 0 0
macse_p (117) 79224 146046 990 31321 284 (2.42 \(\pm\,2.65\)) 9731
needleprot 76561 141036 703 30099 0 0
−0.2 (93) fse0 (12) 60710 109842 510 22691 12 (1.0 \(\pm\,0\)) 668
fse 60407 109170 518 22491 0 0
macse_p (93) 62387 112872 878 23181 252 (2.70 \(\pm\,2.89\)) 8262
needleprot 60270 109122 581 22677 0 0
  1. For varying values of the parameters fs_open_cost and fs_extend_cost, and for each method, the number of CDS pairs displaying a FS translation is given. The values of the criteria for each method are indicated. For each method, the average number of FS_init per alignment, with corresponding standard error values are also indicated