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Table 2 The optimized gap penalties for the VTML200 matrix

From: PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids

Pair-wise sequence identity

Gap initiation penalty

Gap extension penalty

N pairs

0-10%

−17

−1

1,282

10-20%

−17

−1

2,023

20-30%

−16

−1

1,674

30-40%

−16

−1

1,100

Above 40%

−15

−1

705

  1. The column “N pairs” shows the total number of sequence pairs in each benchmark dataset.