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an example for how to align DNA
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9746 7c6358e6-4a41-0410-a743-a5b2a554c398
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‎biojava3-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java‎

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package demo;
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import org.biojava3.alignment.Alignments;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.SimpleGapPenalty;
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import org.biojava3.alignment.SubstitutionMatrixHelper;
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import org.biojava3.alignment.template.GapPenalty;
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import org.biojava3.alignment.template.PairwiseSequenceAligner;
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import org.biojava3.alignment.template.SequencePair;
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import org.biojava3.core.sequence.DNASequence;
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import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
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import org.biojava3.core.sequence.compound.NucleotideCompound;
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public class TestDNANeedlemanWunsch {
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public static void main(String[] args){
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String query = "AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA" +
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"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
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"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
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"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
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"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
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"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
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"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
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"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
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"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
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"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
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"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
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"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
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"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
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"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
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"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
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"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
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"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
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"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
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"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
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"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
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"CCCTTGTGGAGGGAGCCGGTAATTAAA";
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String target = "CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC" +
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"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
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"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
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"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
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"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
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"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
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"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
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"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
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"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
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"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
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"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
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"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
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"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
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"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
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"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
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"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
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"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
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"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
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"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
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"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
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"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";
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GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
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PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(
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new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
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new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
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PairwiseSequenceAlignerType.GLOBAL,
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penalty, SubstitutionMatrixHelper.getNuc4_4());
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SequencePair<DNASequence, NucleotideCompound>
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alignment = aligner.getPair();
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System.out.println(alignment);
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int identical = alignment.getNumIdenticals();
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System.out.println("Number of identical residues: " + identical);
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System.out.println("% identical query: " + identical / (float) query.length() );
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System.out.println("% identical target: " + identical / (float) target.length() );
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}
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}

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