Viewing and managing alignments

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The DNA alignment tool allows you to create alignments to identify regions of similarity and differences in your sequences. You can comment on regions of interest, view alignment statistics, and associated reading frames all within the file. Our selection of options allow you to customize the alignment to your scientific needs, helping you manage everything from the name of aligned sequences to more granular alignment parameters.

View completed alignments

To access and view completed alignments from the sequence entity:

  1. Open the template or consensus sequence file.

  2. Click the Alignment icon in the right-side toolbar.

  3. Select the saved alignment.


To access and view completed alignments from Global Search:

  1. Open the Global Search tool in the navigation bar

  2. Under the Type dropdown, select DNA Alignment

Rename aligned sequence rows

Click on the pencil icon next to each sequence name to edit the name within the alignment file. Editing row names does not change the name of the original sequence entity used in the alignment.


Add and remove comments

To add comments, highlight a base or region, then click Add Comment from the toolbar.

To remove comments, open the comment and click on the trash icon. Alternatively, right click on the comment and select Delete Comment.


View and trim alignment regions

When in an alignment, you can view different regions by clicking and dragging the alignment minimap at the bottom of the screen. To view more of your aligned sequences at once, increase the width of the viewing window.

Drag the black bar on the left and right ends of your traces to trim. The trimmed sections will be grayed out and are ignored when you realign.


View reading frames

Enable reading frames to view which amino acid is encoded for each frame. To enable reading frames:

  1. Click the gear icon in the top-right corner.

  2. Check Reading Frames.

To select which reading frame(s) to keep in the viewer:

  1. Click the gear icon in the top-right corner.

  2. Click the wrench icon next to Reading Frames.

  3. Select the frames to display, then click Save.

If an amino acid differs from the consensus, it is highlighted red. If it's unclear what base is present, those amino acids are highlighted yellow.


Update an Existing Alignment

Alignments are not automatically updated with edits or changes made to the individual input sequences on Benchling. To update the alignment for any new changes, you must realign the sequence. By realigning, you can add new sequences to an existing alignment, update your alignment parameters, or refresh the alignment to use the latest version of your sequences.

To realign a sequence:

  1. Open the alignment and click Realign at the top of the alignment.

  2. In the modal, review your inputs or add new input sequences.

  3. In the Sequences section, check Use Latest Version next to the relevant sequences to update the alignment and include the changes made to the input sequence entities.

  4. Click Next.

  5. On the next page of the modal, click Show parameters. Update and/or confirm the alignment parameters. You can customize the directionality of the sequence here in the Adjust direction drop-down menu.

  6. Check Automatically reindex alignments if needed to view options to reindex the template sequence, if a better index can be detected.

  7. Click Realign.



How are the forward and reverse directions of aligned sequences determined?

The alignment algorithm and the alignment parameters determine the directionality of an aligned sequence. You can customize how the algorithm determines sequence directionality in the Adjust direction drop-down menu in the Parameters tab.

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