Sequence Motif Search

(link to screenshot 10) GeneDesigner permits you to search for any sequence that exists within a construct.

In Sequence View select the “Find” panel (label in screenshot 9)

• Select the “Motifs” tab
• Select a motif from the list, or type a sequence into the “Sequence” box
  • Use IUPAC standard bases to define degeneracies
  • Use {x,y} to permit flexibility within the definitions
    • For example ARGARGN{3,10}VTG = A[A/G]GA[A/G]G followed by between 3 and 10 bases then CTG, GTG or ATG
• Click the “Find” button
  • Results are displayed in a hit list, which displays the position of each sequence or motif found
  • Clicking on the sequence / motif in the hit list highlights the site within the local sequence window
• Initiate a new search by clicking on the “back/clear” button

• The default settings are to search for the selected sequence / motif within every construct in the project
• To limit the search to a single construct, or just a part of a construct, select the “Restrict Search” button (label in screenshot 9).
  • Selecting this button will restrict the search to constructs or elements that are highlighted in the Navigation Pane.