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Find CRISPR Sites on a Sequence

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How do I find and Score CRISPR sites on a sequence?

SnapGene 9.0 introduces the ability to design CRISPR guide RNAs (gRNAs), and to calculate on-target efficiency and off-target specificity scores via our secure cloud service. To learn more see Accessing CRISPR Cloud Scoring.

SnapGene early release users:  The CRISPR search tool is not feature complete. Contact the support team to give feedback and let us know how this tool works for you.

View a target Sequence

Open and view a target sequence of 5000 bp or less. If you sequence is longer than 5000 bp, then extract the target region to a new stand alone sequence before using "Find CRISPR Sites", see Extract a Region in a Sequence to a New File.

Select the region of interest, then click menu Actions → Find CRISPR Sites.

Set the CRISPR Parameters

Set the CRISPR parameters using in the dialog.

  1. Set a name for the search criteria.
  2. If required refine the location considered for gRNA detection.
  3. Use the dropdown to select the PAM type.
  4. If required revise the default target criteria.
  5. Check the option if you want to calculate on-target efficiency and off-target specificity scores using our secure cloud service. For more information, see Accessing CRISPR Cloud Scoring.
  6. Choose the genome used for off-target specificity scoring.
  7. Click Find CRISPR sites to start the scoring and annotation process.

The dialog will remain open until the scoring and annotation process is complete. Progress will be reported under the progress bar.

View the Results

If required, toggle the Show CRISPR Sites button on. If there are a large number of CRISPR sites then the results will be hidden in Map View.

Up to 50 primer binding sites and CRISPR guides can be shown in the Map view. Primers are given priority. If the space is insufficient then CRISPR search results will be hidden. Switch to Sequence view, or Choose to Focus on a region of the Map View to see the CRISPR sites.

In Sequence or Map view, hover over a predicted gRNA to see key details for the site.

Select a site and switch to CRISPR view to see the site in the CRISPR table.

  1. Toggle column headers to sort by that column.
  2. Click the button to choose which columns to show in the table.
  3. Scroll left/right up/down to view the information.

Revise or Save the Results

Select the "Selection Criteria"  tab to perform a new search, or modify an existing search.

  1. Click Find New Guides to create a new search with new criteria.
  2. Click the Edit button if you wish to revise the existing criteria and repeat the search.
  3. Click the vertical ellipsis if you wish to remove the selected gRNA set.

Click menu File → Save to save the results with the target sequence file.

 

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