Hi!

I would like to compare 2 dna sequences and display the differences in nucleic acids on a screen and then convert this/these particular difference(s) in codons.

Here is how I display the alignment, I'm a little bit confuse on what to do on the following steps

private void alignment() throws CompoundNotFoundException {

        String targetSeq = Reference.getRefSequence();
        DNASequence target = new DNASequence(targetSeq, AmbiguityDNACompoundSet.getDNACompoundSet());
        String querySeq = Sequence.getSequence();
        DNASequence query = new DNASequence(querySeq, AmbiguityDNACompoundSet.getDNACompoundSet());

        SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();

        SimpleGapPenalty gapP = new SimpleGapPenalty();
        gapP.setOpenPenalty((short)5);
        gapP.setExtensionPenalty((short)2);

        SequencePair<DNASequence, NucleotideCompound> psa = Alignments.getPairwiseAlignment(query, target, PairwiseSequenceAlignerType.GLOBAL, gapP, matrix);

        this.AlignmentResult.setText(psa.toString());
    }

Thanks a lot in advance for any answers, suggestions or advices!!