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Table 7 Pairwise similarity scores and number of FS translation regions computed by the methods

From: Aligning coding sequences with frameshift extension penalties

fs_open_cost Method C1-002 vs B1-001 C1-002 vs B2-202 B1-001 vs B2-202
−10 fse0 0.42 (1) 0.58 (2) 0.45 (1)
fse (-1) 0.33 (1) 0.27 (1) 0.18 (1)
fse (-0.5) 0.37 (1) 0.43 (1) 0.31 (1)
fse (-0.2) 0.40 (1) 0.52 (1) 0.39 (1)
macse_p 0.40 (4) 0.54 (6) 0.44 (1)
−20 fse0 0.39 (1) 0.54 (1) 0.41 (1)
fse (-1) 0.36 (0) 0.24 (1) 0.14 (1)
fse (-0.5) 0.34 (1) 0.39 (1) 0.28 (1)
fse (-0.2) 0.37 (1) 0.48 (1) 0.36 (1)
macse_p 0.33 (4) 0.47 (6) 0.35 (1)
−30 fse0 0.35 (1) 0.50 (1) 0.38 (1)
fse (-1) 0.36 (0) 0.20 (1) 0.11 (1)
fse (-0.5) 0.36 (0) 0.35 (1) 0.25 (1)
fse (-0.2) 0.33 (1) 0.44 (1) 0.33 (1)
macse_p 0.27 (4) 0.39 (6) 0.29 (1)
needlenuc 0.16 (23) 0.35 (15) −0.36 (1)
needleprot 0.38 (0) −0.12 (0) −0.13 (0)
  1. Normalized pairwise similarity scores and number of FS translation regions computed by the five methods for the 3-CDS manually-built benchmark composed of CDS FAM86C1-002, FAM86B1-001 and FAM86B2-202 (Similarity scores are normalized by dividing them by the lengths of alignments)