Extract a Restriction Fragment from a Sequence
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 the lessons entitled 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.
Save the File
Click File → Save to save the sequence.
View the File
Extracted restriction fragments will have phosphorylated 5' ends and will have single stranded overhangs if non-blunt cutters were selected.