Hi Wim, thanks for tracking this down. I agree, something does not look right here. I'll try to see what is going on...
Andreas On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet <[email protected]> wrote: > Hi all, > > I've been trying to generate some global alignments with biojava and > comparing them with what needle returns. Doing this, I can't seem to > reproduce needle's alignment with biojava. The score returned from biojava > seems to be worse than that from needle, so I'm not sure what's happening > here. > > The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid > spamming people, let me know if you want one). I align them with: > GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4); > PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = > Alignments.getPairwiseAligner( > new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()), > new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()), > PairwiseSequenceAlignerType.GLOBAL, > penalty, SubstitutionMatrixHelper.getNuc4_4()); > SequencePair<DNASequence, NucleotideCompound> > alignment = aligner.getPair(); > > This gives me an alignment with only 23% similarity and a gap at the end. > Varying the gap penalties can give me a gap in front too, but that's about > it. When aligning in needle, I get a sequence with a higher score (6784 vs > (-)5862) and 94% similarity (which seems closer to home). Needle I just run > with defaults (so it uses EDNAFULL) and a go/ge of 14/4. > > Could this be a bug or am I misunderstanding some of the options? > > BTW, if I use a really large gapextend, say -4000, I also get a nullpointer > exception. > > TIA, > Wim De Smet > > -- > Wim De Smet > http://www.straininfo.net/ > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
