>BaeI generates 3' overhangs on both sides so DownstreamEndType equals 1
>(OVERHANG_3PRIME).
i don't think so. you can refer the record in rebase database.
<1>BaeI
<2>
<3>(10/15)ACNNNNGTAYC(12/7)
5'
3'
N N N N N^N N N N N N N N N N A C N N N N G T A Y C N N N N N N N N N N N
N^
^N N N N N N N N N N N N N N N T G N N N N C A T R G N N N N N N N^N N N N
N
3'
5'
the left side should be OVERHAND_3PRIME=1, and the right side should be
OVERHAND_5PRIME=0
the code runs ok for me.
>I just found another bug. In RestrictionEnzyme.java, the first public
>constructor calls the second constructor where "cutType = CUT_COMPOUND;"
>overwrites the attribution of cutType in the first one.
you can read the codes in the first constructor
public RestrictionEnzyme(String name, SymbolList site,
int dsForward, int dsReverse)
throws IllegalAlphabetException
{
this(name, site,
null,
new int [] { dsForward, dsReverse });
cutType = CUT_SIMPLE; #########it has been changed back
}
the last situation you recommended, i am not very sure about it cause i have no
chance to try it.
only my own opinion!
furthermore, English is not my native language. but hope it can still convey my
meaning.
thanks
zhenqing ye
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