ORFs

To display open reading frames (ORFs) in the Linear or Sequence views:

Click on the Translations and ORFs tool ( ) and make a selection from the ORFs sub-menu.

Displayed ORFs appear as color-coded boxes and lines. Multiple ORFs can be displayed on the same line, and stops and starts appear within the color-coded boxes for each ORF. ORFs will change as you edit the sequence. When ORFs wrap across a line break or, in the case of a circular sequence, across the “end” of the sequence, there is no end marker at the end of the frame. Symbols within ORFs have the following meanings:

	Start codon in top frames
	Start codon in bottom frames
	Terminator as start in top frames
	Terminator as start in bottom frames
	Terminator (stop codon, end of ORF)
	Sequence start (linear sequences only)
	Sequence end (linear sequences only)
	Invalid base (non IUB code) in ORF

To hide a single ORF strand, right-click on the strand and choose Hide ORF Strand.

To specify search criteria for ORFs and designate which ORFs should appear in the views, choose Sequence > ORF Detection Options. The selection criteria specified in this dialog are used by the Edit > Find and Find Again when searching for an ORF. Use Minimum ORF size to set the smallest number of amino acids that make up the ORF. Choose whether to show ORFs with or without a start codon, or both. Click OK.

To change the display style for an ORF:

Right-click on it and choose Edit ORF Style. Or double-click on the ORF to select it and choose Sequence > Edit ORF Style.

In the ensuing dialog:

• Check Line to turn on the outline for the ORF. Change the line color by clicking on the corresponding color box.

• Use the Weight drop-down menu to set the thickness of the line.

• Check Fill to have the ORF use a fill color, if the shape permits one. Set the fill color by clicking the color box to the right of the Fill option.

• Check Shadow to have the ORF use a shadow. Set the shadow color by clicking the color to the right of the Shadow option.

*Note: The other options on this dialog are not available for ORFs.

Click Apply to apply the changes before closing the dialog.