After viewing the results on the Process and Review page, you can use the real-time optimization feature to edit the oligonucleotide sequence, make changes to the processing method, and reprocess the experiment without leaving the Process and Review page.
Prerequisites
- For an oligonucleotide analysis experiment, you have processed your experiment and are viewing the Process and Review page.
Procedure
- On the Process and Review page, expand the Real-Time Optimization title bar to view the Sequence, Component Detection, Identification, and Customize Results subtabs.
- The Sequence pane expands and displays the Oligo Sequence Map area (left side), which displays the oligonucleotide sequence, and the Sequence area (right side), which displays sequence information including the variable/terminal modifications for the currently open analysis.
RTO pane for an oligonucleotide analysis experiment - To edit the Sequence, Component Detection, Identification, and/or Customize Result subpages, select the corresponding subtab to open the subpage and edit the parameters.
- On the Sequence subpage, select Edit to open the Oligonucleotide Sequence Editor and edit the input oligonucleotide sequence and modifications. To save your changes, select Save As New and type a new name for the edited oligonucleotide sequence in the New Sequence Name box.
- On the Component Detection subpage, select a task from the Select Task to be Performed drop-down menu and edit Basic/Advanced parameters related to the detection of components in your analysis.
- For more information on these parameters, see Edit the Component Detection page.
- On the Identification subpage, edit the Oligonucleotide Identification, Advanced Search, and Ribonuclease parameters by selecting the individual subtabs.
- For more information on these parameters, see Edit the Identification page.
NOTE
The ribonuclease options "Nonspecific" or “None” are not supported for theoretical digestion at this time.
Thus, if you enable the Customize Results subpage of the Real-Time Optimization pane to view theoretical digestion results, do not use these ribonuclease options.
- On the Customize Results subpage, select the Enable Customize Results checkbox to activate the Theoretical Digestion and Alias Naming feature.
- Once enabled, you can apply a custom naming scheme to your oligonucleotide components and customize theoretical digestion parameters.
- After entering the appropriate parameters, select Apply.
- For more information of these parameters, see Edit the Customize Results page.
NOTE
The Enable Customize Results checkbox can only be selected if an appropriate ribonuclease was previously selected on the Identification subpage of the Real-Time Optimization pane.
The ribonuclease options "Nonspecific" or “None” are not supported for theoretical digestion at this time.
Thus, if you enable the Customize Results subpage of the Real-Time Optimization pane to view theoretical digestion results, do not use these ribonuclease options.
- When you are finished editing the Real-Time Optimization parameters, select Process in the command bar of the Process and Review page.
- In the Reprocess Experiment dialog box, enter the experiment and method names.
- You can choose to save the experiment under a new name or overwrite the existing experiment. You cannot overwrite an experiment that is currently submitted to the run queue or is actively processing or canceling.
- You can choose to save the method under a new name or overwrite the existing method (unless the method is a default processing method, which you cannot overwrite).
- For both the experiment name and method name, use only alphanumeric, space, underscore, and/or period characters.
- If the application finds invalid parameter entries, an error dialog box appears indicating the parameters that must be changed. To continue, enter the required parameter values within the appropriate ranges and select Process again to proceed.
Reprocess Experiment dialog box - Select Reprocess.
- The application clears the previous results on the Process and Review page and submits a new processing job including your changes to the run queue.
- The RTO job moves to the top of the run queue, behind the currently running job. If no job is currently running, the application reprocesses the RTO immediately.
- While the new job is processing, you remain on the Process and Review page.
- When reprocessing is completed, the Process and Review page automatically displays the new results.
- For more information on the features and navigation of the Process and View page, see Viewing the Process and Review page for oligonucleotide analysis.
NOTE
If you open another results file while the application is reprocessing your experiment, the application will not automatically update the display with the results of the reprocessed experiment.
In this case, you can open your reprocessed experiment in the run queue by selecting the experiment name and then selecting Open Results or by double-clicking the experiment name.