Parts for Modular Sequence Design

Saif Hakim

Benchling now supports parts. 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

The premise of parts is simple: you should be able to make changes to a sequence once and propagate those changes to any constructs containing that sequence.

In designing our parts system, we optimized for simplicity. Every (non-empty) sequence can be used as a part.

Try it out!

Using the parts system is simple. 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 propogated.

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.

Final words

High-throughput design methodologies are becoming increasingly important in genetic engineering. However, with scale comes uncharted complexity. We want Benchling to help you manage that complexity as both your team and sequence library grows.

Parts are a building block for better design tools. From generating large mutant libraries to combinatorial assembly, you can expect great things in the coming months.

With that said, here are a few parting words: happy cloning!

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