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Table 3 Parameters used in Alignment Penalty Function

From: High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH

Name

Factor

Exponent

p align

1.

1.20648

p AA subst

0.5947

11.11090

p break

1.0964

1.60294

p insert

0.5025

2.28409

p insert@term

0.3360

2.28409

  1. The table shows the alignment penalties used for structure and sequence alignments by SABERTOOTH. The values are relative to alignments using the contact vector defined on C α distances with contact threshold dth = 17 Å and three suppressed diagonals nD = 3. These are the same parameters used in [4] for structure alignment.
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BMC Bioinformatics

ISSN: 1471-2105

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