The Sequence section allows you to select color schemes for sequences in the Sequences view. Each available color scheme is described below:

Color by Chemistry - The default color scheme used by multiple DNASTAR applications. Amino acids are colored according to their side chain chemistry. While Color by Chemistry can be used for nucleotide sequences too, we recommend instead using a Solid background color for nucleotides and then selecting a Comparison like Color only nonconserved residues, Color only differences from reference, etc.

Shapely - This color scheme matches the RasMol amino acid and RasMol nucleotide color schemes, which are, in turn, based on Robert Fletterick’s “Shapely models.”

Taylor - This color scheme is taken from Taylor and is also used in JalView (Waterhouse et al., 2009).

Zappo - This scheme colors residues according to their physico-chemical properties, and is also used in JalView (Waterhouse et al., 2009):

Solid – These scheme colors residues with the color shown. After selecting Solid, you can specify the color by clicking on the colored box to the right of the menu.

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