How do I color nucleic acid sequences based on nucleotide properties?
SnapGene (8.1 and later) provides three nucleotide color highlighting schemes as detailed below. These color schemes are available for DNA and RNA sequences. These color schemes are not currently available for pairwise or multiple sequence alignments.
To choose a color scheme, view a DNA or RNA file, switch to Sequence view, then click the "Show Colors" dropdown in the side toolbar to choose between the alternative schemes.
GC Content
Nucleotides are colored according to their hydrogen bonding/pairing, see https://en.wikipedia.org/wiki/GC-content.
Purine/Pyrimidine
Nucleotides are colored according to their side-chain chemistry, see https://en.wikipedia.org/wiki/Nucleotide_base.
Nucleotide Colors
Nucleotides are colored to match colors used for peaks in Applied Biosystems Sanger Sequencing chromatograms.