Create an alignment

Open the DNA Alignment Modal

You have three options for opening the DNA Alignment Modal:

  1. Select the sequences you want to align in your Expanded View. In the "More" dropdown, hover over “Analyze”, and select “Create DNA Alignment”.

  2. Click on the Global Create button, hover over “DNA Sequence”, and select “New Alignment”.

  3. Open an existing DNA sequence, find the Alignments button on the right navigation bar, and click "Create New Alignment."

Choose your inputs

Once the Alignment Modal has opened, you will be prompted to add your inputs. Inputs can be uploaded from your computer, selected from existing Benchling files, or created by manually typing in bases. Selected inputs are visible in the “Sequences” section at the bottom of the modal.

Define your parameters

After you have selected your inputs, click on “Next” to define your parameters. Then, select “Consensus” alignment. You can find more information on what a consensus alignment does on Benchling by clicking into the “See more” button.

Create one or more “groups” corresponding to each consensus sequence you wish to create. Add the appropriate inputs into each group.

Finally, choose an alignment program from the dropdown at the bottom of the modal. We currently support the following alignment programs for consensus alignments.

  • MAFFT auto

  • MAFFT 6-mer distance

  • MAFFT local pairwise

  • MAFFT global Pairwise

  • Clustal Omega multiple sequence alignment

You can view and change program-specific parameters by clicking on "Show parameters".

Once you have selected your alignment program, click “Create Alignment”. A pop up toast will appear once the alignment(s) complete. Click “Open”/View” to access your alignment.

If you created a single consensus alignment, you will be directed to the completed consensus alignment file. If you created multiple consensus alignments, you will be directed to the search directory where you will find the list of completed alignments.

View different regions of the alignment

Once the alignment is complete, click and drag the bottom summary (gray bars) to view different regions. Zoom in by decreasing the width of the viewing window.

Add a comment

Misalignments are shown in red in the summary. You can also add a comment by selecting bases and clicking Add Comment at the top of the tab.

View reading frames

Turn on the "reading frames" view to see for each frame which amino acid is encoded. If an amino acid differs from the consensus, it is highlighted red. If it's not clear what base is present, those amino acids are highlighted yellow:

You can select which reading frame(s) you want to keep in the viewer:

View previous consensus alignments

View the consensus alignment again by going to the inventory file that was created, and clicking on the Alignment icon. Then click on the Saved Alignment.

What's next? 

After having reviewed this tutorial, you might want to learn about how to align to a template next.

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