Update a linear DNA sequence start index to match genomic coordinates

When importing linear sequences directly into Benchling from databases like NCBI, Benchling will maintain the genomic coordinates of the sequence. For sequence files that are uploaded using a different method, all sequence indices will begin at 1. To update a linear sequence to match proper genomic coordinates, you can change the start index of the sequence.

  1. When viewing a DNA sequence, click on the "i" info button on the bottom right-hand bar

  2. Change the Start Index to the desired start coordinate

  3. Select Update Information

The genomic coordinates of the sequence will update accordingly. You will see this reflected in the numbering on the sequence axis, where the first number is now re-labeled as the number that was entered in the Start Index dialogue box.

Re-index a DNA sequence to match your desired sequence view

When working with DNA sequences, the imported view may not exactly match how you read or use you DNA sequence in lab. To adjust the the location of the bases relative to the sequence at large, you can re-index the DNA sequence.

  1. When viewing a DNA sequence, right click on the base at which you would like to re-index

  2. Select Re-index

  3. In the New Location dialogue box, enter in the new axial location of which you would like the selected location to inherit. Be sure to double-check your selected location by looking at the Current Location field. Ex.) If you enter 75 into the New Location dialogue box, the selected current location will become the 75th base in the sequence, with all other bases moving

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