Using Biojava, I want to read multiple sequences and make an alignment for distance tree. I tried using cook book but I am getting an error, can anyone help me with this problem?
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.Alignments.PairwiseSequenceScorerType;
import org.biojava3.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava3.alignment.GuideTree;
import org.biojava3.alignment.SimpleGapPenalty;
import org.biojava3.alignment.SimpleSubstitutionMatrix;
import org.biojava3.alignment.template.GapPenalty;
import org.biojava3.alignment.template.PairwiseSequenceScorer;
import org.biojava3.alignment.template.Profile;
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;
import org.biojava3.core.util.ConcurrencyTools;
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.template.Profile;
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.io.FastaReaderHelper;
import org.biojava3.core.util.ConcurrencyTools;
public class CookbookMSA {
public static void main(String[] args) {
String[] ids = new String[] {"Q21691", "Q21495", "O48771"};
try {
multipleSequenceAlignment(ids);
} catch (Exception e){
e.printStackTrace();
}
}
private static void multipleSequenceAlignment(String[] ids) throws Exception {
List lst = new ArrayList();
for (String id : ids) {
lst.add(getSequenceForId(id));
}
Profile profile = Alignments.getMultipleSequenceAlignment(lst);
System.out.printf("Clustalw:%n%s%n", profile);
ConcurrencyTools.shutdown();
}
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());
//seq.doMultAlign();
return seq;
}
}
errors for this code :
I added forester.jar even though its not supporting
Exception in thread "main" java.lang.NoSuchMethodError: org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix.getIndex(Ljava/lang/String;)I
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:186)
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:188)
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:188)
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:172)
at org.biojava3.alignment.GuideTree.(GuideTree.java:86)
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:183)
at org.biojava3.alignment.CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:43)
at org.biojava3.alignment.CookbookMSA.main(CookbookMSA.java:32)
Biojava Code for multiple alignment and Guide tree
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.Alignments.PairwiseSequenceScorerType;
import org.biojava3.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava3.alignment.GuideTree;
import org.biojava3.alignment.SimpleGapPenalty;
import org.biojava3.alignment.SimpleSubstitutionMatrix;
import org.biojava3.alignment.template.GapPenalty;
import org.biojava3.alignment.template.PairwiseSequenceScorer;
import org.biojava3.alignment.template.Profile;
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;
import org.biojava3.core.util.ConcurrencyTools;
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.template.Profile;
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.io.FastaReaderHelper;
import org.biojava3.core.util.ConcurrencyTools;
public class CookbookMSA {
public static void main(String[] args) {
String[] ids = new String[] {"Q21691", "Q21495", "O48771"};
try {
multipleSequenceAlignment(ids);
} catch (Exception e){
e.printStackTrace();
}
}
private static void multipleSequenceAlignment(String[] ids) throws Exception {
List lst = new ArrayList();
for (String id : ids) {
lst.add(getSequenceForId(id));
}
Profile profile = Alignments.getMultipleSequenceAlignment(lst);
System.out.printf("Clustalw:%n%s%n", profile);
ConcurrencyTools.shutdown();
}
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());
//seq.doMultAlign();
return seq;
}
errors for this code :
I added forester.jar even though its not supporting
Exception in thread "main" java.lang.NoSuchMethodError: org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix.getIndex(Ljava/lang/String;)I
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:186)
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:188)
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:188)
at org.biojava3.alignment.GuideTree$Node.(GuideTree.java:172)
at org.biojava3.alignment.GuideTree.(GuideTree.java:86)
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:183)
at org.biojava3.alignment.CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:43)
at org.biojava3.alignment.CookbookMSA.main(CookbookMSA.java:32)
}
There was a problem in Biojava implementation of getMultipleSequenceAlignment(). You need to override the getAlignedSequence method probably.
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