Use the Oligonucleotide Sequence Editor to define the default list of modifications that are applied to oligonucleotide sequence. From the default list of modifications, you can select which modifications will be visible in the Assign Variable Modifications pane. You can also select the items to include in the sublist for quick loading.

Procedure

  1. To open the Oligonucleotide Sequence Editor window, from the BioPharma Finder home page, double-click Sequence Manager in the Experiment Types area.
  2. In the Sequence Manager, select an oligonucleotide sequence by double-clicking the sequence name.
  3. The Oligonucleotide Sequence Editor opens in a new window.
  4. For more information about the panes and parameters in this window, see Oligonucleotide Sequence Editor parameters.
  5. In the Oligonucleotide Sequence Editor window, expand the Assign Variable Modifications pane to view the list of modifications you can apply to the 3’-terminal, 5’-terminal, or nucleotide bases of an oligonucleotide sequence.
  6. For instructions on assigning variable modifications to a sequence, see Manage variable modifications.
  7. Select Load Default Mods to load the default modifications for the 3’-terminal, 5’-terminal, and nucleotide bases in the Assign Variable Modifications pane.
  8. To view or change the default list of modifications, select Define Modification List in the command bar.
  9. The Define Modification List table opens in the Define Modification List dialog box.
  10. The table shows the modification name, formula, average mass, monoisotopic mass, and modification type for each item in the list. You can sort and filter the table to refine the list.
  11. image/svg+xml 1 2 3
    Table in the Define Modification List pane
  12. The modifications listed in the Define Modification List table are color-coded as follows:
  13. Blue: Recommended default modifications. By default, these modifications are set for quick loading and are automatically selected in the Select Default Modification column.
  14. Black: Other default modifications. By default, these modifications are not selected for quick loading and are not selected in the Select Default Modification column.
  15. Purple: User-defined custom modifications. By default, these modifications are not selected for quick loading and are not selected in the Select Default Modification column.
  16. In the Display Variable Modification column, select the checkboxes for the modifications that you want to be visible in the Assign Variable Modifications pane.
  17. Changes to the selections in the Display Variable Modification column are saved when you close the application.
  18. You cannot clear the checkbox in the Display Variable Modification column if the checkbox in the Select Default Modification column is selected for a particular item in the list.

  19. NOTE

    When you add a new custom modification, the application automatically adds it to the table and selects the checkbox in the Display Variable Modification column.

  20. In the Select Default Modification column, select the checkboxes for the modifications that you want to include in the quick loading sublist and clear the checkboxes for the items that you want to remove from this sublist.
  21. See Default sublist of modifications for quick loading.

  22. NOTE

    When you select the checkbox in the Select Default Modification column, the application automatically selects the checkbox in the Display Variable Modification column to add the selected item to the visible default list.

  23. When you are finished defining the default modifications, select Save to save your changes and exit or select Close to exit without saving any changes.