How To Display Amino Acid Ailgnment In Biojava Using Biojava

Question

[joey0214.zhong]

how to display amino acid ailgnment in biojava using Biojava? I'm using Graphics2D to drew amino acid sequences alignment in my biojava application, but it didn't work! it displayed sequence names , but not render aligned sequences.

Answer 1

[andreas.prlic]

I would do this:

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;
    }

}

[joey0214.zhong]

thanks for your help~ already fixed it

Answer 2

[AsoInfo]

Maybe this page can help you...

http://biojava.org/wiki/BioJava:CookBook3:PSA

[joey0214.zhong]

thanks! I already have alignment.