User GuidesSnapGene User Guide Display Options for DNA SequencesSet the Origin Coordinate for a Linear Sequence

Set the Origin Coordinate for a Linear Sequence

How do I alter the start coordinate of a linear sequence?

Set the Origin (+1) Position Inside a Sequence

Use this option if the new start position (+1) lies within a sequence.


Open the sequence file and switch to the Sequence View. Click to place the cursor to the left of the desired +1 position, then click View → Set Origin. In this example, position 598 will be set as the +1 position.

In the "Set Origin" dialog  the cursor position will be automatically selected. Click OK to change the origin to the selected position.

The sequence will now display with the new origin as the +1 position. Sequence preceding the origin will have negative coordinates, starting with -1 (note there is no zero (0) position in DNA sequence coordinate systems).

Set the Origin based on a Larger Coordinate System

Use this option if a sequence is part of a larger sequence. For example, if a sequence is derived from a complete genome and you wish to display the genomic coordinates.

Open the sequence file and click View → Set Origin. Switch to the option "Base numbers start at", type the new start coordinate and click OK.

In this example, the lacI sequence, derived from the genome of E.coli strain K-12, substrain MG1655, origin is set based on the coordinates of the complete genome. On the genomic sequence (Accession NC_000913) the lacI CDS is in the reverse orientation and starts at position 366,428.

The sequence will now be numbered based on the new start coordinate.