Open Reading Frame Search

(link to screenshot 12) GeneDesigner permits you to search for open reading frames that exist within a construct.

In Sequence View select the “Find” panel (label in screenshot 12)

• Select the “ORF” tab
  • Select the codons to use as start codons
  • Select the minimum ORF size to consider
  • Select the codons to use as stop codons
  • Click the “Find” button
    • Results are displayed in a hit list, which displays the position of each ORF found
    • Clicking on the ORF in the hit list
      • moves the display to the start codon and
      • highlights the ORF within the local sequence window
• Initiate a new search by clicking on the “clear” button

• The default settings are to search for ORFs within every construct in the project
• To search for ORFs in a single construct, or just a part of a construct, select the “Restrict Search” button (label in screenshot 12).
  • Selecting this button will restrict the search to constructs or elements that are highlighted in the Navigation Pane.

• An overview of ORFs within a construct can be obtained in the Global and Local Sequence Views by checking the “ORF Graphical Display” box (label in screenshot 12).
  • This graphical display can be exported as a part of a report.