RE: [Biojava-l] Re:topic about RestrictionEnzyme

[george waldon]

zhenqing ye wrote:
>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.


It's a 5'overhang and if biojava says otherwise, it is most probably a bug. It is just confusing because we use the word "end" to describe both the enzyme cuts (end type using biojava javadoc terminology) and the strand termini (termination of a strand either 3' end or 5' end).

- George