[Biojava-l] Problem finding Restriction Enzyme sites

Richard Holland holland at ebi.ac.uk
Tue Dec 18 08:56:36 UTC 2007

Hash: SHA1


Your code is throwing an exception saying that it doesn't know what the
definition for ECOR1 is. This is because the molbio package doesn't
contain any restriction enzyme definitions by default, and you haven't
loaded any into it yet (at least, not in the code fragment you quote).

Before you can use the methods in this package, you need to have made a
call to RestrictionEnzymeManager.loadEnzymeFile() and pass it a
reference to a file containing some restriction enzyme definitions in
REBASE format #31.

Once you've used this method to load a REBASE file containing a
definition for the ECOR1 enzyme, you'll be able to use the code.


Parsa Hosseini wrote:
> 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
> 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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- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

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