To review DNA sequences in Benchling, you first need to input a sequence. You can manually input a sequence or import a sequence from:

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 Sequence, then click New DNA Sequence. The Create DNA Sequence modal displays four options to input or import a sequence and a prompt to save the file to a project or 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, select a folder, and set the topology.

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

  4. Click Create.

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.

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

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.

What's next?

Learn how to view and change display features on your sequences.

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