It is important to understand differently developing backgrounds for different hydrophobicity scales before choosing one method for analysis.
You should be aware of:
The Rose and Janin scales were determined by examining proteins with known 3-D structures and evaluated hydrophobicity as the probability of finding amino acid residues inside of a protein or on the protein surface.
Kyte and Doolittle and Wolfenden scales were derived from the physical and chemical properties of amino acid side chains.
Four scales of hydrophobicity are available for selection. Since four scales were determined by distinguished methods, it may give very different results on some positions in protein sequence alignment.
The change of hydrophobicity of every column (position) in the protein sequence alignment can be displayed in a nicely color format.
There is no up-limit of numbers of input sequences.
Back to main page.