Feature Library Improvements
Feature Libraries allow you to maintain collections of common features you would like to use for auto-annotation, thereby helping keep annotations standard across sequences in Benchling. Feature libraries can be accessed via the Feature Settings of your Benchling account.
a). Export Feature Libraries as a CSV
Navigate to a particular Feature Library and export it as a CSV by clicking the new “Export” button which looks like an arrow in a box (see the red box in the image below).
b). Import all feature types in a single CSV Feature Library import
Both AA and Nucleotide Features can now be imported together in the same CSV. Previously, a CSV Feature Library import only supported one type at a time. Feature Libraries can be imported by clicking on the “Import CSV” button in the top right corner of the screen when viewing Feature Libraries (see the blue box in the image below).
Note: In the Import CSV modal, you have the option to specify a match type of Nucleotide or Protein. This match type will only be used if the Match Type column in your spreadsheet is left blank for a particular feature.
Create a new Part or Sequence with a default informative name
When creating a new Part or DNA Sequence from a highlighted selection of an existing DNA sequence, Benchling will now assign the new part or sequence’s name based on the current sequence and selected indices. For example, creating a new DNA sequence from bases 165-318 of pUC19 will create a new sequence titled pUC19 [165-318].
See an indication when Benchling is working to auto-annotate a sequence
Benchling now shows a loading spinner when searching for features to auto-annotate with, so you know it is hard at work finding annotations to add in bulk to your sequence. To auto-annotate a sequence, open the annotation tool and select the blue Auto annotate button at the bottom of the Annotation modal.
Improved scrolling for Off-Target scores
When clicking into Off-Target scores for CRISPR Guide RNAs created in Benchling, you can now enjoy smoother horizontal scrolling functionality. This will be particularly useful for cases where Gene or Locus name are particularly long.
Properly Bulk Assemble fragments with atypical indexing
Bulk Assembly now properly handles fragments that cross the origin and are reversed, so the assembled product accurately takes these factors into account. For more information about how to use Bulk Assembly see the articles below:
Navigate to Bulk Assembly: https://help.benchling.com/en/articles/3581344-navigate-to-the-bulk-assembly-wizard
Learn the basics of DNA Bulk Assmebly: https://help.benchling.com/en/articles/2865823-learn-the-basics-of-bulk-dna-assembly
Order of items preserved when using Worklists for bulk actions
When using a Worklist to do things like add samples to a table, the order in which the entities were added to the Worklist is now preserved.
Improved performance of loading plates
With improvements made to the Inventory, plates with a large volume of samples (e.g. 384 well plates) now load more quickly.
Attach Primers to DNA sequences using the Benchling API
The Benchling API now supports attaching Primers to DNA sequences — both the oligo ID or the primer bases can be used to attach the primer. Learn more about how to add primers to DNA sequences using this link: https://docs.benchling.com/v2/reference#sequence-resource
Retrieve results using the Benchling API
Results retrieved using the Benchling API can now be filtered by the entity ID of the entity the results were recorded against. Learn more about how to leverage this entity ID filter using this link: https://docs.benchling.com/v2/reference#list-assay-results