Search sequences for features

  • Updated

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 icon at the top of your sequence map. In the drop-down menu, check the ORFs box to view open reading frames on the plasmid map. To customize ORF settings, click the wrench icon.

When viewing ORFs on the sequence map, you can also specify any codon as the start codon.

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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.

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.

Get the reverse complement

To find the reverse complement of a selected section, right-click and choose Copy Special, Reverse Complement.

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