High-throughput design methodologies are becoming increasingly important in genetic engineering; however, with scale comes uncharted complexity. Benchling helps you manage that complexity as both your team and sequence library grow via the concept of parts:

A sequence can be embedded within one or more sequences as a part, such that any changes made to the sequence propagates to all constructs containing that sequence.

Parts are a building block for better design tools. You may find parts helpful if you:

  • Perform complex sequence assemblies
  • Design large mutant libraries
  • Often re-use specific sequences
  • Have lots of sequences and collaborators

Usage

Open any sequence, right click, and select Insert Part. You can insert any sequence from your library as a part.

A gray background will indicate the presence of a part.

To maintain the integrity of the part, the bases and features of the part sequence will be made read-only. To make changes to your part, right click the part and select Edit Part. The sequence will open in Benchling for editing. After editing the sequence in Benchling, you can return to your container sequence with the part edit propagated.

A few caveats

When deleting a sequence that is used as a part, all sequences that contain it will flatten the part. This means that all bases, annotations, and translations that were in the part will now directly belong to the containing sequence.

When a sequence is modified, Benchling stores a snapshot of that sequence to keep a complete history of your sequence. Versions will also snapshot the parts contained within it. On reset to a version, you will be warned if a sequence that was used as a part was modified or deleted:

  • If it was modified, the corresponding parts will be updated.
  • If it was deleted, the corresponding parts will be flattened.
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