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

Table 1 The optimized property weights and gap penalties for the four default amino acid properties

Pair-wise sequence identity	Weight for hydrophobicity	Weight for size	Weight for coil propensity	Weight for thiol group	Gap initiation penalty	Gap extension penalty	N pairs
0-10%	0.7	0.15	0.1	0.05	0.8	0.2	1,282
10-20%	0.3	0.2	0.15	0.35	0.6	0.1	2,023
20-30%	0.3	0.2	0.15	0.35	0.7	0.1	1,674
30-40%	0.25	0.2	0.15	0.4	0.7	0.1	1,100
Above 40%	0.2	0.2	0.25	0.35	0.6	0.1	705

The four default amino acid properties are hydrophobicity [29], size [30], coil propensity [31] and the presence of the thiol group. By default, PR2ALIGN uses the combination of property weights and gap penalties optimized for aligning sequences with pair-wise sequence identity between 30 and 40 percent (highlighted in boldface type).the column “N pairs” shows the total number of sequence pairs in each benchmark dataset.

ISSN: 1756-0500