Oups! My mistake (and apologies) about the understanding of the defination of
overhangs.
thinking for a while and re-diving into the codes, George is right, maybe it's
truly a bug.
the confused codes is the following functions in RestrictionEnzyme.java
...
public int getDownstreamEndType
a.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' GACGCN^ 3'
zhenqing ye wrote:
>For example HgaI GACGC (5/10) indicates cleavage as
>follows:
>5' GACGCN^ 3'
>3' CTGCGNN^ 5'
>it should be 5'-overhang according to biological rule, but
>in the code implementation it's 3'-overhang
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 re
