I've been looking for examples of how to store restriction sites in GFF3 format, but I have been unable to find any. Assuming I use the correct SO term in the third ('type') column, it shouldn't be too hard. My questions are mostly details.
- Should the start and stop positions correspond to the recognized palindromic sequence, or should they correspond to the exact cleavage site?
- When a sequence is digested by a restriction enzyme, do the lengths of the resulting fragments include the sticky, overhanging, single-stranded DNA, or do the lengths only extend as far as the DNA is double-stranded?