Skip to main content

Table 1 Absolute accuracy properties of the best gap costs

From: Logarithmic gap costs decrease alignment accuracy

 

Absolute Identities

 

Log- Affine

Affine

Logarithmic

Minimum

0.383

0.324

0.183

1st Quartile

0.926

0.904

0.512

Mean

0.941

0.925

0.687

Median

0.976

0.970

0.717

3rd Quartile

0.994

0.992

0.874

Maximum

1.0

1.0

1.0

  1. Accuracy is measured via alignment identity. Log-Affine: G (k) = 2 + k/4 + (ln k)/2 (solid) , affine G A (x) = 4 + k/4 (dashed), and logarithmic G L (k) = 1/8 + 8 ln k (dotted).
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us