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Table 3 Example parameters

From: Optimizing substitution matrix choice and gap parameters for sequence alignment

Set

Model

g

e

G

E

Q

Bali

g2

5.370

0.423

  

80.7%

Bali

g4

5.874

0.473

2.332

1.488

81.0%

Prefab

g2

6.914

0.320

  

61.2%

Prefab

g4

6.742

0.476

3.964

0.322

62.3%

TermGaps

g2

6.508

0.133

  

80.8%

TermGaps

g4

5.010

0.635

15.507

0.026

84.2%

IntGaps

g2

5.725

0.304

  

78.3%

IntGaps

g4

5.725

0.304

6.419

3.343

78.4%

  1. Optimized gap parameters reported by POP for the Bali, Prefab, TermGaps and IntGaps sets. Models are g2 (affine gaps) and g4 (different affine penalties for internal and terminal gaps). Penalties are g (gap-open), e (gap-extend), G (terminal gap-open) and E (terminal gap-extend). Q is the accuracy score. The matrix was the full-precision, one-bit unit version of VTML200, one of the best matrices according to the tests reported here.