Use annotations to navigate

While viewing a sequence file in Benchling, click on the Annotations button on your right side panel. 

In the menu that pops up, select the sequences you wish to see on your sequence map. Click on any of these annotations to jump to their corresponding locations on your sequence map.

Find and edit ORFs

Click on the gear button at the top of your sequence map. In the dropdown, check the ORFs box to view open reading frames on the plasmid map.

To customize ORF settings, click the wrench icon.

Search for a specific sequence

To search for a particular sequence (e.g., “ATATAT”), use cmd/ctrl + F. Enter the sequence into the search box.

Edit the number of mismatches in the mismatches box if you wish. The search results will include all sequences that include your exact sequence with up to two mismatches. 

You can also use "N" to represent a degenerate base in the search box.

Navigate to specific bases or regions 

Use cmd/ctrl + G to go to a specific base. 

Use cmd/ctrl + F and type in your start and end positions (e.g., ":30:37") to select known regions of bases.

What's next?

After reading this tutorial you may want to learn how to view and analyze translations.

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