[Biojava-l] Problem finding Restriction Enzyme sites

Parsa Hosseini phossein at umd.edu
Tue Dec 18 06:39:21 UTC 2007


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,


phossein at umd.edu


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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