Managed Lists

GeneDesigner permits you to create lists of restriction sites or sequence motifs that you can use to search for within a sequence, or exclude from backtranslated sequences.

• These lists can be created and edited from the Configure tab.

Restriction sites are managed by creating and editing lists of sites

• Click the “Add List” button
  • This creates a list named “New List”
• Click on a List to change its name

• Sites can be added to a list by selecting
  • the list to be edited in the upper panel
  • one or more restriction sites in the lower panel
    • clicking the “Add to List” button
    • or dragging the sites from the lower panel into the middle panel

• Sequences can be removed from a list by selecting
  • the list to be edited in the upper panel
  • one or more restriction sites in the middle panel
    • clicking the “Remove from List” button
    • or dragging the sites from the middle panel into the trash

Restriction site groups can be used for

• excluding during backtranslation
• searching a sequence for restriction sites

The motif list is a convenient way of storing sequences to be used during backtranslation or sequence searches.

• Click the “Add DNA motif” button
  • This creates a new sequence named “New DNA Sequence”
• Enter the sequence
  • 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 “Add AA motif” button
  • This creates a new sequence named “New AA Sequence”
• Enter the sequence
  • Use standard 1 letter code