Hi,
I've been using the 'molbio' package to do some Restriction enzyme analysis.
I've come across errors when I want to find the corresponding recognition site.
I'd be very thankful if I could be lead down the path to find were I am going
wrong.
Thank you in advance,
Parsa
[EMAIL PROTECTED]
------------------------
try {
SymbolList siteOfEnzyme = DNATools.createDNA("GAATC");
Sequence sequence =
DNATools.createDNASequence("AAAAGAATCTTC", "mySequence");
RestrictionEnzyme re1 = new RestrictionEnzyme("ECOR1",
siteOfEnzyme, 0, 0);
SimpleThreadPool tr = new SimpleThreadPool();
RestrictionMapper reMapper = new RestrictionMapper(tr);
reMapper.addEnzyme(re1);
System.out.println(reMapper.annotate(sequence));
}
catch (IllegalSymbolException e) {
}
catch (IllegalAlphabetException e) {
}
Exception in thread "Thread-1" org.biojava.bio.BioRuntimeException: Failed to
complete search for ECOR1 GAATC (0/0) at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:136)
at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.IllegalArgumentException: RestrictionEnzyme 'ECOR1' is not
registered. No precompiled Pattern is available
at
org.biojava.bio.molbio.RestrictionEnzymeManager.getPatterns(RestrictionEnzymeManager.java:280)
at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:77)
... 1 more
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