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.
- 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
different mRNA bases
||"*" stop codons
||spliced or truncated
|spliced or 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
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
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
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
Henikoff S and Henikoff JG.
Amino acid substitution matrices from protein blocks.