Base Coloring for Alignment Tracks

The Genome Browser's codon coloring feature allows users to quickly validate and compare alignment tracks, such as ESTs or BLAT results. To turn on codon coloring, select the desired option from the Color track by bases pull-down menu.

Color Options

  • item bases - all bases are labeled.
  • different item bases - red: only those bases that differ from the genomic sequence are labeled or colored red, depending on the zoom level.

Bases are colored or labeled according to the genomic sequence. Note that it is possible to show the complement strand, and thus change the base labeling, by clicking the arrow to the left of the base display in the base position track.

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 item bases (if enabled) and then alignment coloring (if enabled). 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.