How do I alter the start coordinate of a linear sequence?
Set the Origin (+1) Position Inside a Linear Sequence
Use this option if the new start position (+1) lies within a sequence.
In this example, position 598 will be set as the +1 position in a linear sequence.
Open a linear (non-circular) sequence file and switch to Sequence view.
Click to place the cursor to the left of the desired +1 position, then click View → Set Origin.
In the "Set Origin" dialog the coordinate of the nucleotide to the right of the cursor will be automatically set.
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.
In this example, the origin of the lacI sequence, derived from the genome of E.coli strain K-12, substrain MG1655, 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 with the final stop codon nucleotide at position 366,428.
Open the sequence file and click View → Set Origin.
Set the "Base numbers start at", to the desired start coordinate and click OK.
The sequence will now be numbered based on the new start coordinate.
