my understanding here.(just my guess)
to be a biologist, it is right for the defination of overhangs in the reference.
but in the case involved in a cut type where the enzyme cuts in two positions relative to the recognition site, i think it's inconvenient to code implementation for
uniform according to biological rules.
you can try more enzymes in the code, maybe you will find the rules of overhangs defination
in the code implementation.
For example HgaI GACGC (5/10) indicates cleavage as follows:
5' GACGCNNNNN^ 3'
3' CTGCGNNNNNNNNNN^ 5'
it should be 5'-overhang according to biological rule, but in the code implementation it's
3'-overhang. i think the defination of overhang in the code implementation is related with
the strand direction.
anyway, it's not harmful to our biological tasks, and not confused for us to solve problems
when we keep the difference in mind.
thanks
zhenqing ye
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