Align to a template

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 choose 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. Once your sequence inputs have been selected, click “Next”.

Define Your Parameters

In the “Define parameters” tab, choose between a pairwise and multisequence template alignment.

A pairwise alignment will make one alignment against the template for each non-template sequence.

A multisequence alignment will attach multiple sequences as a single alignment on the template sequence.

After making your selection, select your template and non-template sequences. Additional templates can be defined for creation of multiple alignments by clicking on the blue “+” icon next to “Templates”.

Select your alignment program at the bottom of the DNA Alignment Modal. We currently support the following programs.

  • 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”.

Complete the Alignment

Once the program is set, 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.

Trim your trace file

Benchling automatically trims your trace file to the point where the peaks start to look clean. You can also manually select the trimming bar and move it with your mouse.

Inspect part of the alignment 

Use the bottom summary view to scroll to the region of interest. Zoom in by decreasing the width of the viewing window.

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 template, it is highlighted red. If it's not clear what base is present, it is highlighted yellow:

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

Add a comment 

You can also add a comment by selecting bases and clicking Add Comment at the top of the tab.

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