Hi -
This does look like an error although I'm no expert on restriction
enzymes. Can anyone else comment?
If you do find the source of the error please let us know.
- Mark
zhenqing ye <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
05/10/2005 03:04 PM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] topic about RestrictionEnzyme
Hi,
I have tried biojava-1.4pre1.zip for my works, but there are some bugs(i
am not very sure)
in RestrictionEnzyme related classes. I have written the following codes:
...
RestrictionEnzyme enzyme =
RestrictionEnzymeManager.getEnzyme("Bsp24I");
System.out.println(enzyme.getName());
System.out.println(enzyme.getCutType());
try{
System.out.println(enzyme.getUpstreamEndType());
System.out.println(enzyme.getUpstreamCut()[0]);
System.out.println(enzyme.getUpstreamCut()[1]);
System.out.println(enzyme.getDownstreamEndType());
System.out.println(enzyme.getDownstreamCut()[0]);
System.out.println(enzyme.getDownstreamCut()[1]);
}
catch(BioException bioe){
System.out.println("some error");
}
...
the output is like that:(# means commention)
Bsp24I (#Name)
1 (#CutType)
1 (#UpstreamEndType)
8 (#UpstreamCut[0])
13 (#UpstreamCut[1])
2 (#DownstreamEndType)
1 (#DownstreamCut[0])
1 (#DownstreamCut[1])
furthermore, the explanation in REBASE version 504 likes the following...
ENZYMES WITH UNUSUAL CLEAVAGE PROPERTIES:
Enzymes that cut on both sides of their recognition sequences,
such as BcgI, Bsp24I, CjeI and CjePI, have 4 cleavage
sites
each instead of 2.
Bsp24I
5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3'
3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5'
This will be described in some REBASE reports as:
Bsp24I (8/13)GACNNNNNNTGG(12/7)
so i think the expected values should be the following for the last three
parameters:
0 (#DownstreamEndType)
12 (#DownstreamCut[0])
7 (#DownstreamCut[1])
is there any one meet this situation and give some commentions, or maybe i
should try me best to go deep into the source codes.
thanks
Zhenqing Ye
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