[Biojava-l] topic about RestrictionEnzyme

[zhenqing ye]

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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