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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.