On Monday 23 January 2006 11:43, wendy wong wrote: > > OK - so you have a single HMM that emits whole columns of an alignment? > > Usually to a lign three sequences, you would use a 3-head HMM where each > > head emits one of the sequences. > > I am not sure if it would work with a 3 head HMM, as in here the > sequences are related to each other by the phylogenetic tree. so if > the sequences order is the same, the column ACC would have a different > likelihood than CCA.
So you already have the alignment from a phylogenetic program and you are using biojava to compute some other statistic over it? > > > You shouldn't be getting exceptions. This is almost certainly a bug. > > Could you send the stack-trace? > > sure, here it is: Thanks. I am not arround untill the end of the week. Could somebody take a look at this? > Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0 > at > org.biojava.bio.symbol.LinearAlphabetIndex.buildIndex(LinearAlphabetIndex.j >ava:108) at > org.biojava.bio.symbol.LinearAlphabetIndex.<init>(LinearAlphabetIndex.java: >66) at > org.biojava.bio.symbol.AlphabetManager.getAlphabetIndex(AlphabetManager.jav >a:1796) at > edu.cornell.bscb.evopromoter.TestingFunctions.main(TestingFunctions.java:61 >) > > I think I don't need the full alphabet of getDNA(), which has 16 > symbols. I reduced it to 5 (A,T, C, G, N), so I can have a state that > contains more sites... While this is a good idea, it actually will be counter-productive in BioJava. The DNA alphabet only has 4 'real' symbols - the nucleotides. The other symbols (n included) are 'virtual' symbols constructed from sets of the 'real' symbols. By introducing 'N' as a 1st class symbol, you have actually grown the problem from being exp(4,n) to exp(5,n) which is probably not what you wanted :-) > > thanks, > wendy Matthew _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
