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
|
Genomic/mRNA codons |
Nonsynonymous 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 codons |
|
|
Details
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/nonsynonymous
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.
References
Henikoff S and Henikoff JG. Amino acid substitution matrices from protein blocks. PNAS.
1992;89(22):10915-10919.