[Biojava-l] Re:topic about RestrictionEnzyme

[yezhenqing yezhenqing]

maybe it's not suitable for me to answer this question. but i am glad to 
share
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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