Optimizing analysis parameters from the results window

The majority of MacVector’s analysis tools use a standard workflow:

  • Make sure the sequence you want to analyze is the frontmost window.
  • Select the analysis function from the Analysis Tools toolbar or from the Analyze menu.
  • A setup dialog appears letting you assign the parameters to be used in the analysis.
  • The algorithm runs and then a Filter dialog appears, letting you choose which outputs you would like to see and optionally apply filters so that only a subset of the results is displayed.
  • Result windows are then opened in a tabbed results window which you can typically interact with.
The Setup dialog shown for the Restriction Enzyme Analysis tool

Optimizing results

Once you have run the initial analysis then for subsequent analysis you can just repeat the analysis you have just done and further filter it. To do so you need to rerun the analysis tool except now select the Results window (at the tab showing the results you want to optimize) instead of the original sequence.

Restriction Enzyme Analysis

For example for Restriction Enzyme analysis the Filter dialog allows you to further refine the restriction enzyme recognition sites found, for example if you started with a broad search but now want to just show sites that are cut a certain number of times, leave a 3′ overhang or 5′ overhang, have a recognition site of a certain length or other filters. This is also useful if your initial search was too stringent and did not find any sites.

The Filter dialog showing many matches as the Setup dialog had a broad criteria
The Results window showing the many restriction enzyme sites that meet that broad criteria.
Rerunning the RE Analysis tool but now from the Results window.
The results after changing Number of Cuts to 1 and only selecting enzymes with a 5′ overhang.

Primer Design

Some tools work slightly different. For example Primer3 will just show you the filtering dialogue with just output options but without any filtering options (as all options are in the initial setup dialog). But you can just click “RUN AGAIN” and the Primer3 setup dialog is shown with the settings exactly as the subsequent run with the same sequence range selected.

Select the Try Again button to repeat a Primer3 analysis from the Results window
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