get pariwise alignment of protein sequences

andreasprlic · andreasprlic · commit e76dcad95639 · 2013-03-02T17:28:23.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@10073 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/main/java/demo/DemoAlignProteins.java b/biojava3-alignment/src/main/java/demo/DemoAlignProteins.java
@@ -0,0 +1,59 @@
+package demo;
+
+import java.net.URL;
+
+
+import org.biojava3.alignment.Alignments;
+import org.biojava3.alignment.SimpleGapPenalty;
+import org.biojava3.alignment.SubstitutionMatrixHelper;
+import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
+import org.biojava3.alignment.template.GapPenalty;
+import org.biojava3.alignment.template.PairwiseSequenceAligner;
+import org.biojava3.alignment.template.SequencePair;
+import org.biojava3.alignment.template.SubstitutionMatrix;
+import org.biojava3.core.sequence.ProteinSequence;
+import org.biojava3.core.sequence.compound.AminoAcidCompound;
+import org.biojava3.core.sequence.io.FastaReaderHelper;
+
+public class DemoAlignProteins {
+
+	public static void main(String[] args) {
+
+		try {
+			String uniprotID1 = "P69905";
+			String uniprotID2 = "P68871";
+
+			ProteinSequence s1 = getSequenceForId(uniprotID1);
+			ProteinSequence s2 = getSequenceForId(uniprotID2);
+
+			SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
+
+			GapPenalty penalty = new SimpleGapPenalty();
+
+			short gop = 8;
+			short extend = 1;
+			penalty.setOpenPenalty(gop);
+			penalty.setExtensionPenalty(extend);
+
+
+			PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman =
+					Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.LOCAL, penalty, matrix);
+
+			SequencePair<ProteinSequence, AminoAcidCompound> pair = smithWaterman.getPair();
+
+
+			System.out.println(pair.toString(60));
+
+		} catch (Exception e){
+			e.printStackTrace();
+		}
+	}
+
+	private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {
+		URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));
+		ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);
+		System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());
+		return seq;
+	}
+
+}
