[Biojava-l] Re:topic about RestrictionEnzyme

[mark.schreiber at novartis.com]

If there is a consensus on how to fix this problem (if there is a problem) 
let me know so I can check it in to CVS.

- Mark





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-l-bounces at portal.open-bio.org
05/17/2005 04:44 AM
Please respond to george waldon

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        RE: [Biojava-l] Re:topic about RestrictionEnzyme


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

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