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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
05/17/2005 04:44 AM
Please respond to george waldon
To: [email protected]
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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