How does SnapGene calculate conservation scores for a protein multiple alignment?
A conservation score for each position in a protein multiple alignment is calculated by the method of Valdar [1,2]. Perfect conservation yields a value of 100%.
1. Valdar WS, Thornton JM, 2001 Protein-protein interfaces: Analysis of amino acid conservation in homodimers. Proteins 42:108-124 PubMed.
2. Valdar WS, 2002. Scoring residue conservation. Proteins 48:227-241. PubMed.