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()
{
if (dsCutPositions[0] > dsCutPositions[1]) //if
dsCutPositions[0]>dsCutPositions[1], it should be OVERHANG_3PRIME
return OVERHANG_5PRIME; //to fix it, we can change
the ">" to "<" or change the OVERHANG_5PRIME
else if (dsCutPositions[0] < dsCutPositions[1]) //vice versa
return OVERHANG_3PRIME;
else
return BLUNT;
}
...
to ensure the judgement, the following code in the same class is right for job.
so i am sorry for
my mistake. ^_^
...
public int getUpstreamEndType() throws BioException
{
if (cutType == CUT_SIMPLE)
throw new BioException(name + " does not cut upstream of the
recognition site");
if (usCutPositions[0] > usCutPositions[1]) //this is right
return OVERHANG_5PRIME;
else if (usCutPositions[0] < usCutPositions[1]) //this is right
return OVERHANG_3PRIME;
else
return BLUNT;
}
...
thanks for George ^_^
thanks for all
zhenqing ye
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