Argo DNA Sequence Panel

The DNA Sequence panel shows marked up DNA sequence for selected features, or segments. It is a tab on the Inspector panel.

For compound features, the foreground color of exons is blue, of introns, black. Any non-canonical splice junctions will be drawn with a red background. If non-canonical splice junctions or other problems are detected, the font of the dna tab label will turn red. Mouseover the tab to read details about the error condition.

As with all Inspector panel sequence windows, highlighting a region in the DNA Sequence panel also highlights it in the feature map, so you can easily orient yourself in both scales. A valid fasta header is provided for easy copy and paste into other applications.

Right click to see DNA panel specific options, described below:

Name Description
Copy Copy highlighted sequence to clipboard.
Find Matching Pattern... Use regular expressions to highlight matching sequence.
Splice Site Profile Show the Splice Site Profile for this feature.
Make Highlighted Sequence Intronic For editable features, change highlighted sequence to intronic.
Make Highlighted Sequence Exonic For editable features, change highlighted sequence to exonic.
Set 5' Context... Select number of nucleotides on 5 prime end of feature to draw. Default is 0. These surrounding nucleotides will be drawn in orange.
Set 3' Context... Select number of nucleotides on 3 prime end of feature to draw. Default is 0. These surrounding nucleotides will be drawn in orange.
Show Quality (Broad Internal Use Only) Low quality nucleotides are given backgrounds in different shades of red, the redder background the poorer the quality. Mouseover to read exact quality scores.
Superimpose Overlapping Features... Select tracks from which to draw overlapping features on the dna panel. Overlaps will be drawn by setting the background color to that of the track.
argo dna sequence panel

Last Updated: Sept 18 2006
Contact: Reinhard Engels
argo-support@broad.mit.edu