Updating indexes on DNA sequences

Indexes on DNA sequences help assess the relative location of bases on your linear and circular sequences. Keep your indexes updated in Benchling to more easily manage your sequences.

This article explains:

  • Updating the index of a linear sequence

  • Re-indexing a circular DNA sequence

Update a linear DNA sequence start index

When importing linear sequences from databases, Benchling maintains the genomic coordinates of the sequence. For sequence files uploaded using a different method, all sequence indexes begin at 1.

To update a linear sequence to match genomic coordinates:

  1. When viewing a DNA sequence, click i at the bottom of the right-side menu to open the Information panel.

  2. Enter the new start coordinate in the Start Index field.

  3. Click Update Information.

The updated genomic coordinates are reflected in the numbering on the sequence axis.The first number is re-labeled as the new Start Index number.

Re-index a circular DNA sequence

When importing circular sequences, Benchling retains the origin set in the imported file and linearizes circular sequences at the start index position prior to any alignment. Unexpected alignment results, like misalignments at the terminal ends, might occur if the index of your template sequence bisects the non-template sequence(s).

You can re-index a circular sequence by manually updating the start index or using the indexing tool to automatically find a better index, if one is detected.

Update the start index of a circular sequence

To reindex a circular sequence from the sequence map, linear map, or plasmid view:

  1. Right-click the base to re-index and select Re-index.

  2. In the modal, enter in the axial location you want the location to inherit.

  3. Confirm your selected location in the Current Location field.

    • For example, if you enter 75 into the New Location field, the selected current location becomes the 75th base in the sequence, and the location of all other bases adjusts accordingly.

Re-index a circular sequence in template alignments

To automatically re-index a sequence:

  1. In the template alignment, click Realign in the alignment toolbar.

  2. Confirm your inputs and click Next.

  3. At the bottom of the Define parameters tab, check ​​Automatically reindex alignment if needed.

  4. Click Realign.

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