Importing DNA sequences

  • Updated

To review DNA sequences in Benchling, you first need to input a sequence. You can manually input a sequence or import a sequence from your computer, a database, or a genomic locus. 

This article also covers supported sequence file types.

Get started creating the sequence file

To begin inputing a sequence:

  1. Click + in the left sidebar to open the Create menu.

  2. Hover over DNA / RNA Sequence, then click New DNA / RNA Sequence. The Create DNA / RNA Sequence modal displays four options to input or import a sequence, select the nucleotide type, typology, and prompts to save the file to a folder.

  3. Select the sequence input method by clicking:

Input a raw sequence

To manually input a sequence:

  1. Click Create New.

  2. Enter the sequence name, set the nucleotide type and topology, and select a folder.

  3. In the Bases text box, paste the sequence from your clipboard (recommended) or type it manually.

  4. Click Create.


Import a raw sequence using a Registration table

To import a raw sequence in a notebook entry:

  1. From the Insert menu in the toolbar, select Registration table.

  2. Select Create new entities or Register existing entities depending on if you want to import new entities or register existing, unregistered entities.

  3. Select the Registry schema for the entity. A table preview will display for you to review before inserting into the entry. Use this to confirm your selection.
    • If you select a DNA sequence, a Bases column populates next to the Entity Name column. 
  4. Enter information about the entity into a row of the Registration table. Each row corresponds to one entity. 
  5. Click Submit to register the entities. 

Note: The columns of the table are defined in the Registry configuration.

Import a sequence file from your computer

To import sequences saved to your computer:

  1. Click Upload Files.

  2. Select the folder to save your sequence to.

  3. Click Choose a file and select the file(s) from your computer, or drag and drop the file(s) into the box.

  4. (Optional) In the menu that displays after uploading the file, update the file location, sequence topology, or tags associated with the file, as needed.

  5. Click Open Sequence to open the file, or click Close to close the modal.

Tip: If you don't have a sequence to import but want to practice uploading sequence files, download pBR322 to your computer.


Import a sequence from an external database

To import sequences from external databases, click Import From Database and enter the name of the gene.


You can specify different IDs depending on where you want to import the sequence from. We support these inputs for pulling active DNA sequences from external databases:

  • Addgene URL

  • BioBrick ID

  • Ensembl ID

  • Gene name or symbol

  • iGEM Registry

  • Joint BioEnergy Institute (JBEI) ID

  • NCBI Accession Number


Tip: If searching by a gene name returns a result in Ensembl, you can update the transcript or select multiple transcripts.


Import a sequence from a genomic locus

To import a sequence by genomic region:

  1. Click Select Chromosomal Region.

  2. In the Genome text box, enter your search terms to find active genomes. You can search by common name, species, or version.

  3. Select the chromosome and the start and end loci of the target sequences.

  4. Select the folder to save your sequence to.

  5. Click Import.

Supported sequence file formats

Benchling supports many common and proprietary file formats. We’re continuously expanding our list of supported formats, so we always recommend first trying to upload your file into the importer.

Tip: If you encounter an import error because of an unsupported file format, try to save your file or export it as GenBank and FASTA files. These are the most common file types and fully supported by Benchling.

Benchling imports the sequence, annotations, and comments for all of the formats shown below. Multi file types support multiple sequences. Benchling automatically splits the file to import these sequences individually. Trace file types are results from Sanger sequencing, and contain chromatogram traces along with quality data when imported as an alignment.


Importing other file formats sometimes work, but users should depend on them working with caution.

Tip: If you an encounter an import error, ensure your file extensions are formatted correctly.

Custom fields for GenBank Files

Some properties on GenBank features are standard, like /notes, /type, and /label, but GenBank allows users to encode their own properties to store user- or customer-specific data. In Benchling, these custom fields are user-defined name/value pairs. This enables users to import, store, edit, and export all data associated with GenBank features, while modernizing the experience of creating, editing, and managing annotations and translations in Benchling.

When importing a GenBank file:

  • Features of type CDS create translations

  • Features of any other type create annotations

  • Genetic codes on translations import as /transl_table properties

  • Custom fields, where present, are captured, viewed, and editable in the Features panel. You can access the Features panel by clicking the flag icon in the right-side menu.


When a user exports a GenBank file:

  • Translations export as features with type CDS

  • Annotations export as features with their type as specified in the Features panel

  • Custom fields, where present, export as features

Unsupported File Types

At this time, Benchling doesn't support .pdf, .doc, .docx file types. To import sequences in these files, we recommend manually copying and pasting the bases into Benchling.





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