[Biojava-l] aligning sequences with ambiguous bases

[Wim De Smet]

Hi

(sorry if you get 2 copies, I sent this to -request by mistake)

Apologies if this has come up before, a quick search didn't turn 
anything up.

I'm attempting to do a pairwise alignment between two DNA sequences 
using biojava 3. When I try to construct a DNASequence from a string 
that contains an ambiguous base though (in this case 'y'), I get the 
following stacktrace.

Exception in thread "main" 
org.biojava3.core.exceptions.CompoundNotFoundError: Compound not found 
for: Cannot find compound for: y
         at 
org.biojava3.core.sequence.storage.ArrayListSequenceReader.setContents(ArrayListSequenceReader.java:196)
         at 
org.biojava3.core.sequence.template.AbstractSequence.<init>(AbstractSequence.java:88)
         at 
org.biojava3.core.sequence.DNASequence.<init>(DNASequence.java:64)

Should I attempt to mask them somehow? What's the best way to deal with 
these?

cheers
Wim
-- 
Wim De Smet
http://www.straininfo.net/