Codon and Base Coloring for Alignment Tracks

The Genome Browser's codon coloring feature allows users to quickly validate and compare alignment tracks, including mRNAs. To turn on codon coloring, select the desired option from the Color track by codons pull-down menu.

Color Options

  • genomic codons - codons are labeled and colored according to the genomic sequence
  • mRNA codons - codons are labeled and colored according to the aligned sequence
  • nonsynonymous mRNA codons - codons are labeled and colored according to the aligned sequence. Only nonsynonymous codons are labeled. Conservative and non-conservative substitutions are defined using the BLOSUM62 score matrix. Conservative substitutions (yellow) are defined as positive BLOSUM scores, while non-conservative substitutions (red) are defined as negative scores.
  • mRNA bases - bases are labeled.
  • different mRNA bases - only those bases that differ from the genomic sequence are labeled and colored.

Color Legend

mRNA codons
mRNA codons
mRNA bases/
different mRNA bases
red "*" stop codons non-conservative
codon substitutions
base substitutions
yellow   conservative
codon substitutions
cyan spliced or truncated
partial codons
spliced or truncated
partial codons
green start codons
incl. methionine
black "X" truncated

The codon reading frame is defined by the genbank CDS annotation of the aligned sequence. Each codon is colored and labeled in the direction of transcription. A sequence without a CDS will not be colored; these can be non-protein coding RNAs or an mRNA where a CDS annotation was not provided in the original data.

The mRNA bases/different mRNA bases display options are colored and labeled in the direction of the genomic sequence. Note that it is possible to show the base complement, and thus change the base labeling, by clicking the arrow to the left of the base display or by clicking the "reverse" button.

When zoomed out past the base level, the browser will choose one color to represent many bases. The priority of display, from most important to least important, is: different mRNA base/nonsynonmous codon coloring (if enabled), and then alignment coloring (if enabled). The browser will not display genomic/mRNA codon coloring when viewing large regions of the genome. To view labeling, the track must be zoomed to within 3 times the base level.

For information about alignment insertion/deletion display options click here.


Henikoff S and Henikoff JG. Amino acid substitution matrices from protein blocks. PNAS. 1992;89(22):10915-10919.