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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)