How do I extract a restriction fragment from a larger sequence to a new file?
Select a Restriction Fragment
Open the source sequence file and ensure relevant restriction sites are displayed on the sequence. For more information on adding enzyme sites see Choose an Enzyme Set and/or Choose Enzymes Manually.
In Map view or Sequence view, select the first enzyme site, then shift-click on the second site to select the restriction fragment that will be extracted to a new file.
For circular sequences in Map view the order of site selection is important. Reverse the enzyme site selection order if you select the wrong fragment. Alternatively, click Edit → Invert Selection.
Extract the Selected Region to a New File
Click File → New File from Selection....
Enter a name for the new file, choose to "Preserve original original numbering" or leave this option unchecked to reset the first nucleotide coordinate to 1. Click New File to create a new (unsaved) file comprising the selected region.
View and Save the File
Extracted restriction fragments will have phosphorylated 5'-ends and will have single stranded overhangs if non-blunt cutters were selected.
The partial restriction enzyme site left due to digestion will be bracketed, for example <XbaI>.
Click File → Save to save the sequence to an appropriate location on your computer.
