Create a DNA sequence

Click Global Create, hover over DNA sequence, and select New DNA Sequence.

There are four ways you can import a new DNA sequence in Benchling. Below, we will discuss the two most common ways to do this.

Import Existing DNA Files to Benchling

After clicking, New DNA Sequence, click the Convert Files tab to drag and drop your existing DNA files to Benchling. In addition to GenBank and FASTA file formats, Benchling supports file types from common DNA editors, such as ApE, DNASTAR Lasergene, Geneious, Vector NTI, MacVector, SnapGene, and Serial Cloner. You can view all file formats supported by Benchling here.

Import from external databases

After clicking, New DNA Sequence, click the Search External Databases tab. You can directly import DNA sequences by typing gene name, NCBI accession number, or ENSEMBL ID. Once you type in the name of the gene, you can then select the desired genome and transcript annotation.

Customize sequence view

Split Workspace

Toggle Split Workspace at the bottom of the screen to view the DNA sequence and its map at the same time.

Arrange tabs

Drag tabs to rearrange their order.

Customize display

Click the gear icon on Sequence Map, Linear Map, or Plasmid Map to customize what the map displays.

View and create annotations

Click the Annotations button in the right sidebar to view all annotations.

To create new annotations, click New Annotation, highlight the sequence of interest, give it a name, and click Save Annotation. There is a more detailed tutorial in this article.

You can also import feature libraries and perform auto annotation. Learn how to do it in this article.

Find restriction enzyme cut sites

Click the Digests button in the right sidebar to search for restriction enzyme digestion sites.

Enter 1 under Find Enzyme to find all single cutters (learn more ways to find cut sites here). Select enzymes of interest to view them on Sequence Map. Click Run Digest to simulate a virtual digest.

Create primers

Click the Primers tab in the right sidebar to view existing primers or create new ones. You can design primers manually or using the primer wizard. You can also search from existing primers and attach them on the sequence.

View edit history

Use the History tab to view the edit history. You can edit the name of the version so it is easy for you to keep track.

Align sequences

Click on the Alignments button to align sequences. Use Create New Alignment to align your sequence with .ab1 files or perform a consensus alignment.

Design CRISPR guides

Click on the CRISPR button to design guide RNAs or view existing guide analyses. We typically recommend you starting from scratch to ensure all settings are correct. View our tutorial or the blog post series to start your design.

Search DNA sequence

To search for a particular sequence, use Ctrl + F in Windows or Command + F in Mac to open a search window. Click on the gear icon for additional options, such as searching for amino acid sequences or allowing mismatches.

Perform cloning manually or with Assembly Wizard

You can perform cloning manually by copy and paste or use Benchling's Assembly Wizard for Digest-and-Ligate Assembly, Gibson Assembly, and Golden Gate Assembly. Click the Assembly Wizard button at the bottom of the screen to initiate a new assembly.

Create an amino acid sequence from translation

You can directly create an amino acid sequence from a DNA sequence. First, create a protein translation directly on top of a DNA sequence. Then right click on the translation and select Create AA Sequence to create an amino acid sequence.

You can learn more about how to align, analyze, and export amino acid sequences here.

Share a read-only sequence

Similar to a Notebook Entry, you can share individual read-only DNA or amino acid sequences by clicking the Share button in the upper right corner of the screen.

Rename file, change topology and re-index

Finally, click the Information tab to rename your sequence, toggle the sequence's topology between linear and circular form, or re-index your sequence.

What's next

Now that you know how to use the Molecular Biology Suite, you might want to learn how to

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