Argo Analyze Menu

This page describes each menu item in the Argo Analyze menu.

 Menu Item  Shortcut Active If... Description
Align feature(s) selected Brings up a window that lets you run a simple alignment on the selected features.
Show Matching Intronic Edges for Selected Feature(s)* feature(s) selected Highlight matching intronic edges in rest of map for selected feature(s).
Hide Matching Intronic Edges* feature map active Hide any intronic edge highlights.
PolyA Signal View* feature(s) selected Show polyA signal view for selection(s).
Splice Site Profile* feature(s) selected Show splice site profile for selection(s).
Codon Usage feature(s) selected For each selected feature, show the ORF size and percentage of codons beginning with A, C, T, and G.
View Multiple Alignment alignment span feature(s) selected Internal calhoun database only. Shows a marked up nucleotide level multiple alignment.
Jython Scripting Window always Brings up an embedded Jython Interpreter for interactive scripting.
Run QA Feature Analysis feature(s) selected Runs a battery of tests to see if selected features look like potentially valid transcipts.

* Available on right click in the Feature Map window.


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