/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
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*
* http://www.biojava.org/
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*/
package demo;
import org.biojava.nbio.alignment.Alignments;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.SimpleGapPenalty;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
public class TestDNANeedlemanWunsch {
public static void main(String[] args) throws Exception {
String query = "AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA" +
"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
"CCCTTGTGGAGGGAGCCGGTAATTAAA";
String target = "CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC" +
"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";
GapPenalty penalty = new SimpleGapPenalty(-14, -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();
System.out.println("Alignment: "+ alignment);
int identical = alignment.getNumIdenticals();
System.out.println("Number of identical residues: "+ identical);
System.out.println("% identical query: "+ identical / (float) query.length());
System.out.println("% identical target: "+ identical / (float) target.length());
}
}