Create a feature library for auto-annotation

A feature library is a collection of annotated features cataloged as individual sequences used to automatically annotate features across multiple sequences. Labs can use feature libraries to standardize annotations across sequences and share their libraries with other organizations and users.

This article explains how to create a feature library by importing a .csv file and how to add existing annotations to a feature library. 

Note: Benchling supports nucleotide and amino acid sequences, including degenerate bases. Custom fields and genetic codes for amino acid features are not currently saved on annotations in feature libraries.

Create a feature library

You can create a feature library from within any sequence.

To create a feature library:

1. Click the flag icon to open the Features panel.

2. In the panel, click Edit feature libraries in the bottom-right corner.

3. Enter your library name and description, then click Create Feature Library.

   • Enter your feature(s) manually

   • Or by importing features in bulk

Enter individual features manually

To enter individual features to a new library:

1. Enter the feature name and type, then enter its bases.

2. Select a color and classification as protein or nucleotide.

3. Click Add Feature.

Import features in bulk

You can import features in bulk via .csv or ApE library file (.txt). Note that .xlsx files will result in an error. Before importing, ensure your .csv file is formatted correctly.

To import features:

1. Click Import CSV or Import from APE in the top-right corner.

2. Select the feature library to add them to from the drop-down menu.

3. Select which classification to assign unclassified features, then upload the file.

4. Click Upload.

Tip: You can create a new library from the import modal by selecting Create new library from the feature library drop-down menu.

Formatting .csv import files

Format the .csv file with the following column headers:

• Name

• Feature

• Type (optional)

• Color (optional) - hex color codes are accepted in the format #000000

There are 16 colors to choose from when assigning colors to annotations. Hex color codes assigned to features on an import file are mapped to the closest one of these colors:

The table below is an example of required .csv file formatting.

Add existing annotations to a feature library

You can add existing annotations to a feature library in the Features panel expanded view. To add existing annotations:

1. Click the flag icon in the right-side menu to open the Features panel.

2. Click Show Expanded View.

3. Select the annotations to add to the feature library.

4. Click the save icon in the top-right corner.

5. Select the feature library to save the annotations to, then click Save Features.